My books in QuickBooks are a mess. Should I clean them up before I switch?

No. Pick a cutover date, say the first of next month. Import what you have from QuickBooks Online through that date, connect your bank and credit card accounts from that date forward, and have Elliott reconcile from there.

If the old balances are wrong, fix the opening balances once rather than rebuilding two years of history. Clean from the cutover forward and treat the past as a single adjustment. Your QuickBooks file stays exactly where it is, so nothing is lost if you ever need to look back.