I would expect to enter a transaction into an account register. Then for a category, I would choose a category rather than an account unless it the transaction was a transfer.
When you choose a category, there should be a scroll bar to the right of the list of categories. You can use that to scroll. alternatively, use the up/down arrow keys or the PgUp or PgDn keys.
If that does not match what you are asking, please list what you click to get to the point where you are doing the action that you have a problem with.
What version of Money are you using? Would you like to use 2-level categories?