Structuring Jira for automated time-tracking for R&D Credits, CapEx, and OpEx

[Jordan Lampe]

I see this discussed online, but almost 0 (aside from this 3-part piece from Rally) on how to structure and configure a software management tool to enable time-tracking automation. To be clear, I'm not talking about automating stopwatch-like time-tracking. I'd like to explore how others have structured their instance to use velocity, points, transitions, nature of work, initiatives, etc. to automagically surmise the hours tracked to eligible efforts. 

Many videos, like this, elude there's a GAAP/IRS approved precedent for this approach, but, again, not a lot of chatter that pulls back the curtain on how it can/should be done. 

I have a few ideas, but anyone got advice?