I made a lesson about how to connect to the soundcard here:
Connecting To Soundcard
As far as the effects go, I would try doing both methods (using your amp for effects and plugging your guitar straight in and using plugins for effects) and see which way sounds better.
I'm going to try to make a post this weekend using some of the free effects mentioned
here with audio clips, preset files, and little info about using some of the plugins. So you'll be able to get an idea of the sounds these plugins are capable of.... Which is very good!
-tkr