ok, so the command prompt
In Windows, it's in Start -> Programs -> Accessories -> Command Prompt. Or you can do Start -> Run -> type in 'cmd'
In the command prompt, you want to change directory to the directory where bspc is, so for example if gtkradiant is in c:\gtkradiant\
cd \gtkradiant
then type what I said in the above answer.
bspc -bsp2aas c:\quake3\baseq3\maps\mymap?.bsp
this runs the program, and lets you also start it with command line options (like '-bsp2aas')
If you need more help with using the Command Prompt, go
here