how assign pagination to one of three loops on page?

I have a homepage that features 3 loops. Two show posts of a specific category and the third one is the main loop. But it seems as if the two category loops screw up pagination for the main loop.

The same happens on my archive. I’d like to use 2 loops on the archive template. Again pagination is screwed up. Seems as if pagination gets confused by the small loop on the sidebar.

Any idea how to assign pagination to a specific loop? Or hide a loop from pagination?

Thanks for any help! I couldn’t find any so far and I’m beginning to get really desperate …

(see https://pastebin.com/525841 for code)