First of all, what does your favorite CD routed into the Bose sound like? My guess; bass heavy.

The issue is likely with the Bose, not the rest of your stuff. Get the subwoofer out of a corner or away from the wall - I'm guessing that's where it was when you auditioned your setup.

This is true for any PA, but even more critical with the Bose because they often tell you to put the system BEHIND (read - closer to a wall than other PA systems) the performer. They even crow about this in their instructional videos.

You can get instantly different results just by moving the system around in the room - and there's the rub, you won't know the ideal location for the Bose in the performance room until you are there with all your gear.

You shouldn't have to do a bunch of EQ to your stuff. It's the Bose in your auditioning space, and if you are setting it up at home for audition, you likely don't have a room that's big enough to try out how to use it as if it's in a larger performance space.

For the computer output, put an EQ plugin on the output bus to reduce the bass for while you are auditioning at home, but likely turn that EQ off when you go to your first gig.

That's my read on it. Those Bose systems are great for gigging, but likely problematic with home use. You are experiencing that, IMO. Again, try a favorite non-bass-heavy CD through the Bose, without moving it from it's current location. My guess is that you will say it's bass heavy with that well-done CD. It's not the CD, and it's not the CD player.