If you have not imported your entire purchase and sale history you will need to enter your current holdings for each security/bond/mutual fund/etc that you own. There are two ways of doing so: Manual Entry and Starting with a Current Balance.
The most straightforward way to enter your holdings is to manually input all transactions from the first date of purchase to the current date into the register. This will allow Moneydance to track capital gains.
Starting with a Current Balance
If you feel you have too many historical transactions to enter manually, or prefer to start from your current balances, you can do so. It is important to remember that if you start from the current balance and don't enter all the historical transactions, Moneydance will not be able to track capital gains. If this is the method you choose, you must enter some form of "Buy" transaction for all the shares of each security you own in the account. To add your current holdings for a security you can enter a Buy transaction for the total number of shares you currently own using the current market value. For example, if you own 50 shares of XYZ stock, enter a single Buy transaction for 50 shares (even if you purchased them over time), using the current market price. You could also enter the original basis for the stocks and the appropriate number of shares, which permits better tracking of your ROI. Repeat for each of your securities. Once you have entered each of your securities this way your account will show a large negative cash balance. To correct this, go to Account->Edit Account (make sure you're in the account you want to edit) and enter the cash balance number as the starting amount in the Initial Balance field (without the negative sign, of course).