There are a couple things you can do. You can delete those accounts and maintain any linked entries in accounts you don't want to remove. It will prompt you to keep those linked entries in other accounts or delete them when you delete a specified account. I encourage you to read the instructions regarding that prompt carefully so you make the right choice. It is a 50/50 chance you will get it right if you don't read it
I would 'Save Changes' under the File menu first, and then delete the account while choosing to save linked entries in other accounts. If you make a mistake or its not giving you the results you were intending, you can force quit CheckBook to revert to your last saved state of your accounts file.
The other option if this sounds too permanent would be to lock it. You can do this by double clicking on the account in the accounts drawer and entering a password in the general tab. This will hide the balance in the accounts drawer and now allow you to view the contents of that account without a password. This is helpful if you just want to remove the balance from your overall total and protect its contents, but it will not give you back space in your accounts drawer. It will still be visible, but with a lock where the account balance would be.