http://www.simulanalog.org/
Well respected and free Marshall and Fender amp sims here plus some stomp box sims.
Also some JS amp sims included with Reaper.
You can just insert your amp sim of choice as an effect on your track. Look at the User Guide section on using effects in reaper if you need to.
http://www.cockos.com/reaper/userguide.php
Then if you wish you can chain together stomp boxes in front of the amp sim (or after if you wish) just as you would with real amps and effect boxes.
There are loads of threads on amp sims on here but if I were you I might just muck about with one or two sims to start with until you've got the basics of how to get the best out them. It would be very easy to get overwhelmed with the options out there, even if you stuck to freeware.
Good luck and let us know how you get on.