Without an actual screenshot of the register I'll have to make a guess at this...
Does the 'Unconfirmed' transaction pane appear at the bottom of the register?
Does it state the number of unconfirmed transactions?
If so, drag the pane upward to reveal the unconfirmed transactions.
Click the split window icon next to the 'New Transaction' button in the upper, right-hand corner of the register. Doing so, will integrate the unconfirmed transactions into the register.
The 'screwed up' balance may be the result of the need to enter or edit that account's 'Initial Balance' or 'Initial Debt' (depending on the type of account).
While viewing the account in question, from the Moneydance menu bar, go to Account > Edit Account.
Here you can enter or edit the 'Initial Balance' or 'Initial Debt' value.
Just to add to Kevin's comments. With a combination of manual and downloaded transaction you should run through the confirmation process, which includes the ability to merge downloaded and manual transactions where necessary.
While there are similarities between Quicken and Moneydance in many places it will never be the same. I was effectively a Quicken user and it did not take to long to adapt to the differences and to often use them to my advantage.