I plan on getting two mics and running them into an Alesis USB or Firewire Mixer and then running the mixer directly into the PC for recording.

My current setup is a Toneport GX, and what I like about it is that it intelligently routes the send/returns of the guitar signal, my regular Sound Blaster card does not do this.

So my question is does the Alesis USB/Firewire mixer operate like a standard PC sound card or does it actually control the send/returns like the Toneport?
When you use any type of interface it bypsses your stock card on the PC so you get better recording and playback.

The USB interfaces will take up to two mono inputs (two mics) at one time but any more than that and it will mix down to a single stereo track.

With firewire you can get interfaces with 8+ inputs and it will record them all on a separate track. Larger interfaces like the PreSonus firestudio will also have a lot of outputs so you can use them for monitors and headphones.

BTW, most of the time mixers, (even firewire and usb units) are not very useful in a studio setup...a proper interface will do just fine as your sequencer software always has a mixer in it.