I have the same issues with the debits and credits being interchanged. So am awaiting an answer on that.
But regarding the 1/1000 amounts, that is due to the delimiter. While importing, select the decimal rather than the comma as a separator.
I found a work around. Moneydance now has a problem importing QFX data from TD Credit Card. It worked fine for years prior to November or December of 2019, but something has changed. Until they figure this out, I have been able to export data from TD Credit Card to a csv file. I then open it in excel, add a column to the right of the amount column, move the credit amounts into this new column and import. This gets the charges and credits into the correct columns.
I followed your instructions below and downloaded my December transactions from TD Credit Card Services but it did not fix the problem. The charges are all in the payment column and the payments, or credits are all in the charge column. Also the payments are off by a factor of 1000. A 1,000.00 payment imports as 1.00. There are other problems as well, the download included payments, divided by 1,000, from three or four prior months. It also imports duplicate transactions. Importing via QFX is not working for me at all. I am going to stick to importing by .csv file and modify it as I described below.