To make gil from the market, first you need to understand how it works, or else you will end up stalling your retainers with stuffs that doesn't sale and make next to nothing when you do.

The principle is simple, supply and demand. It isn't about who undercut you by how much, it is about whether or not there is a demand on the items you are selling. Giving 2 players full stacks of something, one can sold them in a day with high profit while the other makes no gil and wasted spaces of their retainers.

If you are still with me, then the question should be "so what makes a difference?" The answer is simple but it takes a little research, just like reality. First, you need to know who will buy it and why they buy it for.

The 101:
Lets pick Silver Ore for example. There is only one class that uses them, Goldsmith, which is to make Silver Ingot. Say you have a full stack and wants to sell them, the simplest way is to sell the full stack and 1 gil lower than the lowest in the market. That is not the optimal approach as a) Someone else will undercut you in the next 10 minutes, b) You ain't making as much as money as it would, and c) the demand is low as the supply is high.

Instead, sell it 1, 2, 3, 6, 12 at a time as 3 ore makes 1 ingot. The reason of selling in 1-2 pieces is due to the fact that sometimes people have 1-2 left in their inventory and wants to free a slot. Now since you are selling at a quantity that actually fills people's demand, you don't need to undercut. In fact, if there are no one or very few people selling at these quantities, you can actually put in a healthy markup and people will still purchase them as it saves them from a) a slot, or b) the afford of reselling left overs.

Yes, you only have 40 slots and that reduces the number of inventory on shelf, but what is more important? Selling stuffs or having a lot of stuff on sale? A retainer with 20 slot open > a retainer with 0 slot open. The key is that you maximize profit on each sell with minimal shelf time.

Since you have limited shelf spaces, focusing on selling 1 type of goods ain't going to get you far. Instead, you can spread the net by covering different ores to ensure that inventory moves. Get 1-2 stacks of each ores and sell them with the above method and you will see that your inventory moves every time you visit your retainer.

102:
Now ore isn't high yield goods and 100% markup of 1 gil is just 2 gils, as you start making gils, you can move up a level and start selling more expensive stuffs, the ingot. Yes, if you are a goldsmith yourself, you can turn ore to ingot and sell them, but the same principle still applies, supply and demand. The key isn't about your crafting profession here but your skill to sell stuffs. Once you understand how the market works, you will see that there are lots of dead goods in the market that are not moving. You can simply purchase them in high quantity and starts to make gils by breaking quantities down or produce them yourself and sell in the correct quantities. The key is knowing what people use the goods for and what quantity make sense to consumers.

Crafters needs to buy goods as it doesn't make sense to go out and farm 2 ores and come back to craft. In fact, crafters need goods from other crafters and they often only need a small quantity of a specific mid-tier crafting mats. By knowing what these mats are and the quantity that people actually needs, you can sell them with markups as the markup saves them work and inventory spaces, like ingot, as Goldsmith is not the only class that needs them, but is the only class that can make them. Selling mid-tier mats makes far more gils than raw mats, but you will quickly fine that inventory move so fast that you lost track of what they are and how much you sold them for. You will need to come up with an inventory system as well as a inventory movement projection system to ensure that you have everything for sale with finite storage space.

Here is the challenging part, assuming that you got the quantity, how much shall you sell them? Well, you will need to do a shelf time analysis on it. If they are selling like hot cakes, it means there are room for a higher markup. If you can do it systematically by logging the average shelf time, then you can maximize your profit.

103:
Instead of purchasing high quantity and break them down, it is also viable to purchase in small quantities and sell them as a batch. This method requires more investment, lots of guts and monitoring. Materias are produced one by one, but crafters usually use 10+ a time as people upgrade their whole body. Camp the market for new inventory, purchase them, and sell them as a batch with a handsome markup.

In fact, if you have established a working pricing system, you will be able to see what is under priced in the market. This makes "buy low sell high" possible.

104:
At this point you should be wealthy and process more gils than you know what to do with it, but if you are obsess about it, there are still lots of ways. Get into a FC and make friends with people with a profession, be it gathering or crafting. Eliminate auction cuts by having gatherers sell raw goods directly to you, in turn you tell them what to farm. Then you can a) sell raw goods to crafters or b) have them craft mid-tier goods for you at a reasonable fee. Clearly, HQ quality is what you after and you can sell them back to other people in FC when they actually needs them or push them out to the market.

105:
At this level, you can expend your item list from mid-tier mids to final items like gears. HQ gears sells more but melded gear sales even more (even low level meld). Those who actually purchase gears are not likely to be capable of making those gears themselves, so they will need to get people to meld them. You on the other hand has established connections to all crafting skills and these connections will prefer to sell things to you over fishing off the market (assuming that your pricing is reasonable.)

106:
By now you should have a reputation in your FC as you are the goto person when it comes to trades. You can start selling gears to people within the FC as different crafting class needs gears, yet again from other crafting classes. As long as your pricing is reasonable, people will start buying off you as your service will save them time to farm, craft and meld. Stock 10 of each melded crafting gears and systematically replenishes goods. Selectively push goods into the market depending on the market's demand/price, at this level you will find everything in the market is either overpriced or no supply.

Clearly you will find that you don't have enough spaces. One way to resolve this is to talk to your FC master for company bank spaces. Do not free anything to anyone including the FC master as that will destroy your business. Having said that, offering huge discount to a point that you lose gil is okay. If you can't establish that, then either upgrade your account or a new FC.

201:
The economy of any game won't entertain you, why not do it for real?