Anytime I go to make changes to an uploaded document, it saves the changes as a "new" document, it seems?
Happy to take your word for that.
Why won't it just save the changes to the original document, instead of creating a new document each time?
The original document is written in a different ‘language’, though the effective difference may be little more than between English and American. Some Excel functions are just not available in Sheets (and vice versa). @Jacob Jan Tuinstra has published comprehensive lists of those that are equivalent and those that are not. However, Google makes allowances for this by converting incompatible Excel formulae to their result values on import. That’s not exactly an answer to “why” but I think is at least a part of the rationale.
With import, changes are saved to the (alternative) ‘original’ file. This can still be saved back to Excel, if required, but again there would be risk of function incompatibility.
do I just have to continually make changes to the "sheet" version instead of the original?
Not if you import the Excel document to Google Sheets (with File, Import…) rather than upload it. One advantage is that this facilitates sharing with people who do not have Excel, I'm hoping that another is that it solves your problem.