After the initial 5 steps, you're answer becomes clear as mud to me.  For Clarity I will  place ** before and after my questions. 

1. You said, " you'll want to proceed to the bank deposit. - ** Does this mean, Hit New and Bank deposit,  or to highlight the actual received deposit in my checking account?**

2. You said, "When in the bank deposit tab (** Which Tab,  where do I find this tab**),

Please answer from here and I will proceed

select the amount you want to include when depositing to the account, and then in the Add funds to this deposit section, enter the appropriate amount to assign to your account. Doing this allows you to split the funds between an account and an invoice.