@chriswade,
install the FSX and register it using it's own registration licence.
Start fsx and fly the default flight - exit FSX
Install the acceleration and register it using it's own registration licence.
Again fly the default flight.
Now start tweaking the settings to suit you and your PC.
As Pete says, there is no reason to not let it install in default location.
If your on a 64bit OS you may have some trouble with addons like aicarriers/2 , you'll need the 32 bit version of Java Runtime Environment and not the 64 bit one as FSX is a 32but program.
It's worth looking at
http://www.venetubo.com/fsx.html for having your fsx.cfg tweaked.
Mentioned eleswhere in the forum.
regards
Steve