Hello hij,
.files folder corresponding to PSX file is always created in the same directory with the PSX file itself and it is not possible to have the same project files saved across multiple locations.
To reduce the project size you may consider removing key points (do not mix with the tie points), depth maps, cropping mesh and dense cloud (use Compact Dense Cloud, if you have removed any points from the dense cloud), removing orthorectified images, unless you require to apply any patching manually.