OK...Before I go about moving 150k+ jpg images ....is this going to be something that will likely change in future builds?
Not likely. Your JPEGs and RAWs may be in folders that are siblings of each other, but they could be on different hard drives (as duplicates, it happens quite often) so joining is only done if the two images share the same folder.
Also if I were to move the jpg files into the same folder as the RAW images would I have to rescan the catalog, or is PM clever enough to know it's the same files.
If you do the moving in Photo Mechanic Plus, it should make everything up-to-date. If you do the moving outside of PMPlus then you'll need to use the Catalog Sync tool (Catalog->Sync Catalogs...)
Is there a way of only showing RAW or JPG files (without adding jpg/cr2 in the search box)?
You could either enter 'and filetype CCR2' or 'and filetype JPEG' to your search terms (without the quotes) and you'll only see CR2 or JPEG files that match the rest of your criteria. You can also Filter by File Type and use a Custom Search Filter to do the same thing but it would be more point-and-click.
-Kirk