Can I upload multiple files for each subsection of my visa application, or should I combine them into one PDF?

Each section only allows one file upload maximum 3 megabytes. If you need to combine multiple pages then do that and compress if needed to fit the file size requirement. There are many free online tools to do this.

From other posts here, yes, that seems to be preferred by the embassies.

I don't recall anyone having a rejection specifically for multiple PDF uploads, but since they never give a reason, I can't say for sure.

Follow the page sequence of the list of required documents and put everything in one file and you should be OK.

I use I Love PDF for these edits. Very good, and free. Good luck.