Correct, Craftsmanship, Magic Craftsmanship, and Control are only for crafting. The other 3 are only for gathering. If you forget, change to a crafting or gathering class, it will only show the relevant stats on your attributes.
As far as what they do, recipes have a specific hidden value of either Craftsmanship or Magic Craftsmanship, never both. If the relevant stat is close to or above the target stat, you'll have a noticeably easier time performing a synth. If you have the money and inventory space, it's not a bad idea to get 2 sets of gear focused on each stat, try your hand at crafting with both sets on each new craft, and swap between them as needed. It will take some trial and error but all items of the same "type" will use the same stat. Example: "Fingerless Leather Gloves", "Fingerless Peisteskin gloves", and "Fingerless Boarskin Gloves" all use the same stat. For most purposes, a balanced set of gear will be sufficient.
Alternatively, if your server crafters provide them you can swap between using Main Hand tools and Offhand tools. Mainhand tools offer more Craftsmanship and offhand provides more Magic Craftsmanship, but keep in mind due to level differences between tools one tool might just be outright better than another.
Control basically effects the stability of a synth. Like the other two, each craft has a hidden target number. If you're above this number you will see less elemental destabilizations and you'll be able to take more actions before seeing aetherial sparks, the latter of which is essentially a message that "you're taking too long!" on a synth (based on the number of actions you've taken) and will really make your success rate drop.
I haven't tried gearing towards specific elements when crafting, but the rumor is that having higher elemental stats reduces your chance at elemental destabilization. However, STR/INT etc are tied to the tools you use, and having a higher relevant stat will boost your HQ rate. You can find which stats are for which tool at the bottom of this page.
As a side note, if you look at the stats for the gathering classes, STR/DEX/VIT make it easier to aim for items for the appropriate class, while INT/MND/PIE increase the quantity of items you get from gathering.
Concerning "Wait", the crafting orb will shine in 4 colors which indicate your success rate if you take an action. From highest chance of success to lowest, it is White, Yellow, Red, Rainbow. However, the lower your chance of success the more potent your increase in Progress and Quality will be, so it's up to you to figure out if you want to risk it. For leveling up a craft or working on things that are quite a few levels above you, it's better to Wait on red and rainbow orbs to let it reshuffle and possibly change the color. Waiting also has a chance to stop elemental destabilizations although some elements (freaking Lightning) may take a while to go away, so depending on how far along the synth is you might just want to soldier on.
That was a lot but hopefully it helps.