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I have a botanist at 15 atm I plan on leveling each crafting class to 20 then move each at 5 level intervals. Is that wise?
All crafts use different shards (main and side), when you get up to higher levels, more shards will be used. So I wouldn't exactly say it's worth it in the long run (you could always farm shards if you're okay with that though).
My bags are filling up with mats from botanist, will my 2 retainers be able to handle to amount of storage?
Err they might be able to depending on what's already in there, I haven't really leveled a DoH class far so I can't speak on this.
Is it best to pre gather or see what I need for DoH then go out and find the stuff?
While it'd be more tedious, yes. You'd be saving yourself a lot of money by gathering your own materials rather than buying them ALL off the AH, but there's no problem with doing that either.
Any tips on keeping mats sorted in bags / retainers to make crafting easier?
You could have one retainer hold all the crafted items, and one hold all your materials (the ones from botany that you aren't using).
Hope some of this helps!