The easiest way is to create a start-miner.bat file with this contents:
echo on
mine.bat stratum+tcp://[pool].com:[port]
Then create a second one called mine.bat with this info:
start C:\Users\username\Desktop\cpuminer-GC3355-win32-fixed\minerd.exe --freq=850 --gc3355=COM1 --url=%1 --userpass=user.1:x
start C:\Users\username\Desktop\cpuminer-GC3355-win32-fixed\minerd.exe --freq=850 --gc3355=COM2 --url=%1 --userpass=user.1:x
etc. This will launch a separate command window for each minerd process from a batch script. If you want to switch pools, just edit the start-miner.bat file and put in a new pool, instead of having to modify each line of your mine.bat file.