Thom,
That ProTools software should work just fine for you.
Some of the pro-audio folks I deal with use hardware recording set-ups, and are unhappy with having to deal with so much ProTools based input. Odd file formats, coupled with portions of audio files missing entirely, being the most common complaints.
(Now, if the guys making those source files with ProTools were paying attention and checked their work before submitting it, information gaps on files would never be passed on. And, if the ProTools users were being considerate, they would pass on the music in a more universal file format like .WAV or .FLAC.)
One interesting benefit of learning ProTools is that it is very similar to Audour in Linux. When you switch to an open-source operating system, you'll already have many of the skills necessary to work with Ardour, Rosegarden, JAMin, and Audacity - and all in a rock-solid, virus-free environment.