Welcome. As an owner of a 2010 MX-5 Grand Touring with a freshly installed carpc, I'm sure I can help!
The factory bose amp is actually line level. If you buy a metra dash wire kit and solder the speaker wires to rca ends and plug them into a sound card you will be fine, I know, I'm doing it.
If you want to remove the amp or just not use it, you are in for a world of hurt. I did the bosectimy on my 2003 mx-5 and it is a ton of work and cost. The NC's don't have direct replacement speakers for the bose system as it is .5ohm and clearwater doesn't make them for the NC.
I have been back by my amp a few times as I installed a custom 8" ported box(I'm a soft top.. hard tops can't have the box). The amp isn't THAT hard to pull out. The hard tops probably are difficult though.
I could blab for hours so hopefully I have answered the question you had. Let me know if you have other questions as I likely have dealt with it recently.