About a year and a half ago I tried to use MoneyDance but found that the UI was too much of a change from what I was used to, and I had a lot of issues with my account data. I am again so frustrated with Intuit and it has been long enough that I decided to try it again, but I am finding that while I can learn the new UI easily enough, there is a big issue that I cannot figure out how to get fixed, and it is not something that I found an easy answer to in the knowledge base, so I thought I would check here.

I have used Quicken for 24 years. I have a lot of data because of all of the accounts and financial institutions over the years. When I imported all of my information into MoneyDance, I find that even if I set the starting balance properly, there is a difference in the balance calculated by the two programs - in one case it was off by a nickel but I have hundreds of transactions to go through so resolving that is not an issue, but in another case it was a negative balance of several thousands of dollars, almost the same amount as the positive balance that the account truly has, and again there are hundreds if not a thousand transactions to go through if I am going to find the difference. So my first question is: Does anybody know of any particular transaction type or transaction issue that MoneyDance definitely handles differently that can cause this? It will be helpful to know if I can look for specific things in transactions.
Next, I hook up online banking to my accounts, and in the case of a credit card account for example, it downloads all of the transactions that the bank has in their history, which was over 300, and MoneyDance does not even TRY to match them up with the transactions already in my register, so now I have over 300 duplicate transactions and it mucks up my register and balance. It would be easy to just delete the downloaded ones marked in blue, but then the software will re-download them the next time. So to keep the ones in blue and eliminate the original ones, I have to edit the category (in some cases) and to do that 300+ times is a nightmare. So again, does anybody know how to force MoneyDance to try to find the transactions it downloaded in the register and match them up?

Should I just give up and start fresh with MoneyDance and use both MD and Quicken until such time as all of my old transactions in Quicken are reconciled?

Thanks