I don't know if anyone's mentioned this before but I thought I'd mention it because it's been saving my sanity lol.
When I'm linking ,up/positioning side by side, modules and find that sometimes I just can't get one to fit into the space I want it to, no matter what I do short of moving content around (to different mods or just adding more (hit or miss) it seems to stubbornly not go back into it's hole.
An example is when I wanted to put an "allposter" (brilliant way to add free/royalty free images into your post!) next to a text file (or next to any module) for some reason it wouldn't stay next to it (even though it was there before I added the contents mod below it.
The fix I'm finding is to insert a new text module move it up through the right panel (summary of where your capsule are) and as you move it to the spot you want to fix you'll notice they start to reposition themselves- one position around there (above or below) will reposition the capsules correctly (or where it was before that worked before adding a module that "disrupted" the herd), at that point drop the text module (put it there).
Return to the spot where you added the text module (in the content area) and simply delete it- don't know why this works but it does, and has every time so far. Another way to do this (but I haven't found success every time with this) is to add the txt module (or use one already in there that's BLANK, around until you see it the way you want it, then drop it. (I go to "page view" to refresh the page at that point then re-enter edit mode and all is good- then I remove the txt mod.
Hope this helps! Good Luck!