Your institution almost certainly should be handling the finances, talk to your department grants administrator. One of the criteria for NIH grants is that you have an institution supporting you and ensuring compliance with all the rules - that's what they're there for. I have a hard time imagining NIH giving R01 money to someone at an institution that doesn't provide that support.
Papers aren't "allocated" to aims, you'll credit the whole grant when you publish papers. In any event, haven't you already written your research plan for how you are going to approach those aims? Your papers will come out of that plan (and the necessary deviations from plan), not from any optimized allocation strategy. Future grants will depend on your ability to write a comprehensive forward-looking proposal and your overall output from previous funding; they won't go through and see that you've completed each and every aim exactly the way you said you would, but they expect you to make progress overall. It's often impossible to actually plan for an entire multi-year research program ahead of time.
Progress reports aren't competitive and won't affect the funds you have, just make sure you do them, and don't lie.
NIH has an extensive website at https://grants.nih.gov/grants/oer.htm all about grants this page specifically for post-award documentation; it's probably worth doing quite a bit of reading there. I'd be wary about depending on books and blog posts because these can quickly become outdated: go to the NIH itself, they aren't hiding their rules to be dodgy and catch you making a mistake, they have rules for a purpose (sometimes more of a legislative/political purpose rather than scientific) and want people to comply with them. It's your institution's job to keep up to date on this stuff (and a bit yours, too, but it's probably a waste of time for every PI to become familiar with every aspect of NIH grant administration - that's why institutions provide the support and why NIH considers this support crucial).