Let's keep digital out of GMRS!! There's no need to make things more complicated so that people can ask for radio checks or kerchunk all day. Just look at the sh!t show we have on the amateur bands with DMR. I'm sticking to analog.
Sounds like you don't have the right com port selected. I run all my Windows based programming software in a VM as I am a Linux user. They all work fine. Some want you to manually select the correct com port.
I believe the rules state 50w maximum. For a base with a good antenna and feedline 5w is more than enough. I have a StationMaster fed with 1/2" Heliax at 50' and I get out just fine. As for an amp, just use what you have as there's going to be no noticeable difference between the two power levels. Invest your time and money into a good antenna system.