I'm not too fond of the J River support forums, but if you are willing to dig a bit, your questions and the answers are likely there.
I'd not be too concerned about JR's install. it'll see what you have for your video and audio just like WMP, ItUNES, OR ANY OTHER media player would.
there's two JR players. Jukebox & Media Center 12. Jukebox is free 100%. Media Center 12 has a 30 day trial. Media Center can play ALL media files. Jukebox only plays audio files. MC plays protected, WMA, iTunes, etc.
I suspect yet do not indeed know, that JR MC (what I use on my XP Pro), alters the path for music playback apart from the Sound Mixer inherent to Windows OS AUDIO playback.
What I do know, is with as crapy a sound card as one can have, the onboard audio became immensely better with no other changes and doing playback simply through my desktop Altec Lansing 2.1 junkie speakers.
gaining a better USB DAC (or in essence, a diff Sound card), playback via a higher res system was again improved.
As I had no ASIO (audio stream input output) driver, I added one of them too... ASIO for all... together, the sound is rivaling my main CDP source... albeit not surpassing it. the immediacy or avialability of the greater variety and access of the tracks on my PCs USB HDD offsets the lessend presentation...
The other installed software media players I have on board werent' affected. I never use WMA... but do use and have installed, ituens, Power DVD, EAC, VLC, & Winamp. so it's doubtful something bad or irreversable will happen if you install JR.
In fact I'D REALLY LIKE TO KNOW IF GREATER GAIN COULD BE HAD USING JR WITH A BETTER ONBOARD CARD, AND i SUSPECT IT WOULD... BETTER THAN WITH usb dac? THAT'S A DIFFERENT TEST.
Good luck, don't worry.