I tend to shoot RAW+JPEG for my timelapses. I work on Mac OS X Sierra. When I get back from a shoot, I manually go through and split the RAW and JPEGS into separate folders. I use the JPEGs to make low-res previews to check if the full RAW timelapse is worth processing.

Is there an automated way to do this? Am I going about this wrong? Any suggestions? Thanks all!

The only reason I see for shooting RAW+JPG is when you use qDslrDashboard for analysing the images. The jpgs are only needed then while shooting. As soon as you import from LRTimelapse with the internal importer, you can check "Skip JPGs" and they will not get imported. The next step would then to load the raw sequence into LRTimelapse, you will get an instant playback option there as well as further tools like the curves and the interval column that will make it very easy to analyze the sequence, split it etc. Check out my tutorial video: https://lrtimelapse.com/tutorial