IN order of importance, here is the list of areas that will affect the quality of the recording on the way TO the digital recorder (PC or otherwise)...
[edit]1) The Instrument[/edit]
2) The players themselves
3) The room they're playing in
4) The mic selection to capture the sound of the player in the room they're playing in
5) the mic pre - which colors (favourably or unfavourably) the mic used to capture the sound of the player in the room they're playing in
6) the A/D converter - which converts the analog signal to digital -- get the sound wrong at this point by using cheap converters, and the digital quality will be diminished a great deal.
[edit]Cables and digital clocking are what ties it together. Crappy cables and clocks are often overlooked until the last moment when everything you spent gobs of money on, and your recordings still sounds like a Radio Shack infomercial.[/edit]
If you get all these steps right, then you'll have a very good digital representation of the sound you fed into the recorder. At this point, the digital audio is uncorrupt and will remain so as long as you don't overwrite it.
S/W generally works non-destructively on audio files unless you intentionally overwrite changes.
If you now load that sound file into a poorly written piece of s/w that doesn't handle DSP operations properly, you'll probably find that the sound differs from what you heard playing back the original file.
By contrast, if you take your digital file and load it into quality s/w, edit and manipulate it, you should notice far less change or deterioration (if any) to the end result.
.) I have some experince with Pro Tools at work but am not sure if it is safe to use something lesser. 
) and write it to the hard drive or does the software just tell the Hardware to record and it all sounds the same no matter what the software?
