How do I enter a beginning balance (manually).

I suggest you enter a self-referencing transfer transaction: open the register, press Ctrl + N, set the date (earlier than the first transaction), payee (for example, Opening Balance) and the appropriate amount.  In the category field, enter the name of the register with square brackets (for example, [checking account]).  You may also enter the category by selecting the register from category field's pull-down menu.