So I am a beginner. I was trained with Final Cut Pro but I've been using Kdenlive for a little while for small projects.

Now I'm doing a bigger project and I am a bit confused. I am using a Canon EOS 60d and an external audio recorder. When I've finished each recording I want to make one uncompressed file from the joined video and audio which I can use in the future. Which render profile should I use to preserve the quality of the video (keeping in mind that I am going to use Kdenlive for most of the editing) for future use. My recording settings have been 1920x1080 24 fps, HD1080p.

Check the lossless render destinations - choose one. The files will get really huge.

Another option you could consider is just to import the .kdenlive file of your joined video and audio project as a clip into a new project. That will do the same without rendering.

Yeah, I found the lossless files rather big. I'll try the project file way you suggest.