Most importers can automatically import deposits and withdrawals.
If this is not the case, you can do this manually on the Transactions page. Please note that these need to be coins that you already own and have been established with a cost base. All other scenarios of sending or receiving coins need to be entered as a different transaction type (see here)
Example:
You have received 0.1 BTC from another exchange or wallet
Create 1 entry: (IN) Deposit of 0.1 BTC
Example 2: You have sent away 0.2 BTC to another wallet or exchange of yours
Create 1 entry: (OUT) Withdrawal of 0.2 BTC
Example3: You have transfered 1 BTC from Wallet A to Exchange B
Create 2 entries:
(OUT) Withdrawal of 1 BTC from Exchange = Wallet A
(IN) Deposit of 1 BTC to Exchange = Exchange B
If fees have been included in your transfers, refer to the examples given in the section: Entering Fees