If you record the entire band to stereo then you're pretty much done - you can add more guitars, vox, and what have you, but you won't have any control over the original instruments.

The stereo method works fine for chamber music and jazz, but as far as rock is concerned you are better off tracking the drums to two tracks and then tracking the remaining instruments.

BTW, what make / model of multitracker is it?

Tascam dp-01fx

I sappose it seems like most drummers iv worked with dont acualy count through the song like there sapposed to, they just kind of go off of everyone else, so when i record they dont play there parts right, is this common, or am i just dealing with some bad drummers?

It's common for upstarts to fall off the meter. I've had to have some serious talks with young guys about that, which typically elicit the following responses: "Well, it's Protools, can't you edit it?", "My buddy has Garageband and blah blah...", "I'm nervous, it's my first time in a real studio; I just need to warm up.", and my favorite "Can't you just take the first verse and chorus and paste them? The guitar player knows the song really good..." (Uh, what about your new bass player, i.e. the sweaty, smelly, pimply faced kid I gotta spend the next 16 hours with, who also lacks any semblance of meter, and doesn't realize that his active pickup (that annoying clicking noise in your headphones) needs batteries to operate properly?)

Anyway, I digress.
You want everyone to play together, but only have two track input capability.
If what you are doing is for a highschool course, you can send the drums to one mono track and the rest of the instruments to another, then overdub each instrument individually using both mono drums and instrument tracks as a guide.

I'd like to say you should hit the principal up for some money to upgrade your recorder, but my father's a teacher - I know how hard that can be.

I'm quite the noob myself, so take this reply more as a restatement of the question than expert advice...

I suppose you could record the whole band live to 2 tracks (1 stereo mix), and then one by one overdub the instruments onto their own individual tracks, eventually discarding the live take. However, unless your players are really in synch with themselves (on the original take) I would think the whole thing could get messy pretty quickly.

Perhaps another approach with the gear you have is to start with a click track (just a simple metronome for the length of the song) and have the band play together, but only record say the bass and guitar/keys direct to 2 tracks (direct, not mic'd so there is no bleed through of the drums or other instruments). BTW, I don't know what your "band" consists of, but I'm assuming fairly straight R&R. Next would be for the drummer to play along with this and record the drums - s/he wouldn't have to count through the tune as the main supporting parts are there. Then go back and record (or re-record) all the other tracks as needed.

Just my $0.02... (don't spend it all at once)
-Mark

Perhaps another approach with the gear you have is to start with a click track (just a simple metronome for the length of the song) and have the band play together, but only record say the bass and guitar/keys direct to 2 tracks (direct, not mic'd so there is no bleed through of the drums or other instruments)...

Next would be for the drummer to play along with this and record the drums - s/he wouldn't have to count through the tune as the main supporting parts are there.

Our old shows were run kinda like that - click to drummer's headphones along with other incidental tracks, sweeteners, voices, cues... The drummer kept the band in time and on cue.
Those guys that played out there, they were friggin' awesome drummers. Most are seasoned session guys. I just saw one of the guys that I admire and look up to more than most the other night. He is just one rockin' dude! When he took to the stage in the morning, I knew it was gonna be a good day to mix! He was on, all the time, never strayed, he just got into a zone and boom! he was goin' - in the pocket, consistent. I could send my talkback mic to his phones and say BS during the show and he'd just look up at me in the FOH booth and laugh, never missing a beat. That kinda guy is awesome to have around. He can keep time on his own, to a click, to the band, doesn't matter...

Perhaps your idea is a valid one.

So would it be better for me to just tell the drummer to learn the song before i try and record them, and i mean the whole song not just "i know how the chorus goes, and i know how the verse goes", but so they acualy know how many times the chorus is played and so on?

You're darn tootin'!