I missed a few skills in The Crater, can I return here after the shell thing is around. I'm guessing I would have to go through gaeas cliff etc. I don't want to get there and find I can't and waste time.

Uh, what disc are you on firstly? Disc 3? If that's the case, then you can easily leave the crater by heading back to the top of the crater (through the small cave at the top of the screen in the first section) and then climbing up to the Highwind. As long as you do this before reaching the bottom of the crater (where your party members hand over the items they've found), you're fine.

Also, a lot of Enemy Skills can only be found on monsters in the Crater (Pandora's Box being the main one, which is only cast once by only the first Dragon Zombie you encounter), so it's worth going through the Crater several times to get everything.

I am on Disc two. Just got the Submarine. It was a bit jumbled what I said. Basically, can I get to the crater with the Highwind and avoid doing the whole Gaeas Cliff part/Snowboarding part. Or do I need to wait until later until that shell thing that repels the highwind has gone.

Yes and no. The whole Gaea's Cliff/Whirlwind Maze section is unreachable once you go through there in disc 2 (once the Meteor is summoned). You can still snowboard down Great Glacier and wander around the snowfields (especially if you missed the Alexander summon materia), but you cannot proceed further past Mr Holzoff's cabin.

So if you missed anything on your way through there the first time, then you're out of luck sadly, as the crater is completely different when you go through there as the final dungeon in disc 3.

I presume the Enemy Skills you're after are Trine, Magic Breath and Bad Breath right? Trine is tricky (one of the trickiest skills to learn), but can easily be gained in disc 3 if you haven't done the Pagoda quest in Wutai (simply equip all Enemy Skill materias you have that lack the spell to Yuffie when she faces Godo at the top of the Pagoda).

Magic Breath however is used by the Parasites in the Crater in disc 3 so you can easily gain it if you missed it the first time. Likewise with Bad Breath - Malboros are quite plentiful in the final dungeon so their signature spell can be gained later too. ;)