Putting a 3.2L into a 5spd car is very straightforward. If they are the same year everything is nearly plug and play. This article has most of the details:
Pelican Technical Article: Boxster Engine Conversion Project - 986 Boxster (1997-04) - 987 Boxster (2005-08)
Downsides:
A lot more heat generated by the larger motor so you will probably want to add the 3rd radiator.
The 986 5spd is not as robust as a 6spd so you may want to add a trans cooler as well if you do performance driving. Good luck with your project.