Is up to you, but you need to know, after replacing the stock Bose player, your dashboard will not look as smooth as stock condition. Furthermore your volume control on the steering will no longer working. I suppose your 2din player come with LCD display, if that is the case, you have 2 LCDs on your car. If you ask me I will say this is a waste because since stock LCD can be connected to additional player, then why install another.
There is a small AMP in your rear boot for your Bose woofer and speakers (diagram attached). I not sure it actually work directly with the woofer or go throw Bose player. I have 94 pages AV diagram of 350z, it is very complicated and seems like the player connected to so many things. I guess the shop technician will not understand how the wires are connecting to each other and they will not spend time to investigate. Normally what the shop will do is to ignore whatever they don't understand and lay a new set of wire to connect to you speakers and woofer, of course, bypass stock AMP and other electronic instruments. They may ask you to get a new AMP as well.
Furthermore, the LCD fix at player area will have glare problem. Stock LCD display position and angle has been calculated in such way to reduce the ratio of luminance between the task and the source of glare.