When you run fmriprep, you should specify an output directory.
If you place your precomputed FreeSurfer results at that point, they will automatically be taken in by fmriprep.
In practice: if you intend to point your outputs to
/some/output/folder, then store the FreeSurfer directory under that folder (
/some/output/folder/freesurfer). The tree should look then like:
Finally, you call fmriprep like
fmriprep /path/to/bids_root /some/output/folder --participant_label <subject_label>