When you apply a tag(keyword) to a file, Phototheca saves tags(keywords) in both two sections of JPEG file: IPTC and XMP sections of JPEG metadata inside the JPEG file. This means tags are kept when you copy files and tags can be read by any software what supports IPTC standard like Photoshop, Aperture, Lightroom, Picasa, Windows Photo Live Gallery, and various online photo sharing sites.
Phototheca respects XMP sidecar files when import photos, so if you have a bunch of RAW files with keywords in XMP sidecar files, Phototheca would read them and take into a count.
Read more:
Keywords overview
Work with metadata