yeah - getting the first batch of anything in a sync mode is always a challenge...
Like the other person, I have been downloading quotes, brokerage, and mutual fund data for decades. I have also added all our checking accts - some grandfathered free, some using the no-charge web connect. And for our credit cards - again using no-charge web connect to download, balance, and categorize the transactions.
I mainly use Quicken for the "investment tracking" aspect. But have recently focused on getting a handle on a "yearly budget" so I'll have a clue as to what we all spend during the year.
I could not do this without a full download of both checking AND credit cards, along with the auto or manual effort to "categorize" each transaction of check written.
Bite the bullet - fix everything up - and let the download rule the data file.