Thanks for your help. I ended up calling support and getting walked through everything. I used to have the problem with everything going into Undeposited funds, and about 18 months ago a friend with bank auditing experience came over and we tried to get rid of it, as I had no idea what it was for. My business doesn't get a high volume of payments... 2-3 orders a month is pretty normal... so I always deposit the check before I report it to QuickBooks.
The rep I spoke to was great... he took the time to explain it all to me... for example I never knew what undeposited funds was. He explained it's a place to report a payment, before you deposit the check. Since I don't operate that way, we removed it and he showed me how to properly re-deposit the checks (I open the 'bulk' deposit, print out its contents, delete it from the register and then go back to each payment and change from "undeposited funds" to my bank's account. Now the transactions show up as of the date I put on the "receive payments" screen.
Thank you again for your help!