You can choose to add your securities (stocks, bonds, funds) manually as a single Investment (Asset Class: Funds, Brokers & Banks / Asset Type: Other) , but because of the nature of custody accounts (having a cash AND a securities component), when tracking transactions some clarifications are required to avoid classifying them incorrectly.  

A detailed explanation is provided below, but the key information is:

  1. with reference to Transactions, you only need to record Deposits and Withdrawals (movements IN and OUT of the account);
  2. with reference to Valuations, you need to update the account valuation each time there is an Income (dividends, coupons, etc) or an Expense (execution or custody fees);

Any movement WITHIN the account (buying securities with the cash in the account, or selling securities and retaining the proceeds within the account) should not be recorded. 

DEPOSIT: if you deposit cash (or transfer securities) into your broker account, then the definition of a Deposit remains valid and you account for it by recording a Deposit transaction. But if you use some of the cash in the broker account to buy securities, there is a Deposit transaction for the securities component and a Withdrawal transaction for the cash component, so - with the exclusion of transaction fees you may be charged to buy the securities (see EXPENSE below) - there is nothing to record as the two transactions cancel each other out.

WITHDRAWAL: the same is valid if you sell securities, but keep the sale proceeds within the broker account. The overall value does not change because of the sale, and you only need to account for a Withdrawal if you transfer the cash OUT of the account.

EXPENSE: an Expense does not change the value of individual Investments, but in the case of Broker Accounts it does, as the cash component goes down in value once that expense is taken into account. So if you are charged 5 USD to buy some shares, you account for it buy updating the valuation of the broker account (reducing it by 5 USD).

INCOME: the same is valid for Income, since the value of the account will be increased by that income once it is received; even though the security component that generated that income has not changed in value because of it, the cash component has - and you account for it by updating the valuation of the broker account.