After using a modelling amp for a few years Im considering getting a head/cab and starting to use effects pedals. However Im sorta confused as to how they will work together. For example, if I had a two channel amp, clean and overdrive/lead or whatever but I wanted to use my own distortion pedal for a crunch sound for example...

a) Could I use the effect only on the clean channel to get the crunch sound..
b) Would I still have to us the channel switcher on the amps footpedal...

Do most players only use the one guitar channel (clean) or not?, if they are using effects

And what exactly is an effects loop

a) yes, in fact many people do that to begin with.
b) You can still use the channel switcher on the amps footpedal to switch between the amps clean and dirty channels.

A lot of guitar players use a one channel amp and push the volume of it until it breaks up nicely. Then you can back off your guitar's volume knob(s) to get a clean sound. If you wanted more overdrive you can add an overdrive pedal in front of that.

Finally, an effects loop allows a player to insert a chain of effects after the preamp but before the poweramp, allowing for modulation effects to modulate the preamplified guitar signal, sometimes providing a better sound.