I assume you want something like:
file001.jpg, file 001.CR2
file002.jpg, file 002.CR2, etc
and you are getting file001.jpg, file002.CR2, file003.jpg, file004.CR2, etc.
Try filtering by file type (library -> filter bar -> metadata -> file type) to select all the files of one type, renaming those, then selecting all the files of the other type and renaming those the same way.
If you take care to run the filter on exactly the same set of files each time (and of course preserve the file suffix while renaming and starting the number sequence at the same point) then you should have what you want.
I've not tested this, so I suggest trying it on a very small number of files at first.
However, I don't see the benefit of importing both jpg and raw of the same image.
I think Don has the right idea, but I don't think you need to employ the filter bar. There's a 'last import' collection made automatically when you import images, so I'd start there and it should have all of your most recently imported images. On the bottom toolbar I'd choose Sort by File Name, then change that to Sort by File Type. If you do that you should have Img001.cr2, Img003.cr2, etc. followed by Img002.jpg, Img004.jpg, etc. Then you can shift-select all of the .cr2 files, go to Library/Rename Photo (or press F2) and enter/edit your file naming strategy, setting the start number at 1. Do the same thing for the .jpg files.