You can place the GPS aerial in the dash, on top of the head unit cage. There is space between the two air vents.
If you have Bose or normal amplified system, then you will likely need either one or two ground loop[ isolators to remove the noise from the phono connections that come out of the HU or get a HiLo filter and use the amplified output speaker wires, so the signal passes through the filter and comes out as a deamplified signal to the amp.
Alternative is to replace the speakers and their wiring, which would allow you to drive them either directly or through an aftermarket amp, but this would be a more adventurous route and will cost a bit more. Results would be much, much better though.