Okay, I just want to know if this is a good Idea.

I decieded that on Emerald version, that i would have 4 teams. One is an 'exploration team' with pokemon who know HM moves for exploring the world, the other two are 'battle teams' who are all level 100 on one team and level 50 on the other. Then, there is a 'capture team' where I have pokemon at different levels/types if i need to capture a pokemon somewhere.

Not quite a good idea; you only need two pokemon for your "exploration" team, Tropius and a water type (I like Marill); between the two you should be able to teach them each and every HM move. It's an interesting idea to be sure, although you don't really need the level 50 team either. I would suggest for sure a Level 100 team and a capturing/exploring team, with a Tropius and a Marill (or your choice of water pokemon) as part of that team.

I agree those to would be albe to get all those hms but then all of there move would be a hm and you would not be albe to change them

Yeah, that's the point. You don't need to change them, you use those pokemon as HM slaves, that compress the moves you need to get anywhere in the world into two pokemon, leaving the rest of your pokemon to train however you want, without worrying about needing the HM moves.
And besides, ever heard of the move deleter? If you wanted to change them, you can, but as I said, there's no reason to.

ya thatz good...i might use marill and tropius, and combine tham with the capture team cause i'll need to explore to capture, so thanks!

one good battlefrontier teams have to be:

a grass/water pokemon
a psychic pokemon
a fly pokemon
and a electric pokemon

then you shouold be able to take on the enemy

I generally only have five Pokemon who are "genuinely" in the team who do the fighting. I leave an empty slot for a Pokemon that I only need for the time being (such as to Fly, use Strength or Rocksmash, Waterfall etc). You don't need to have access to all eight HM moves all the time.

Or, you can always store one or two of your battling Pokemon (I'm sure your other Pokemon in the team can manage without the others). For example, I store my Blissey until I need her in battles so I can leave a spot for someone to Fly and Pick-Up/HM Slave.