There are a couple of variables depending upon how your business is set up. But here's the way that works for most people. But DO CHECK with your Tax Accountant, s/he may have you change the names or move the transactions to a different QBs Acct that they may have set up.
First go to your Chart of Accounts (all the Registers) and see if you have an Equity or Owner Equity Acct. If for any reason it is not there, create an Equity Acct as the Name and also as the Type when you create it.
Next create two Sub Accts which you can call Owner Investment and Owner Draw. When you get done it should look like this:
Equity
- Owner Investment
- Owner Draw
When you enter the deposit in the bank, the owner's name is the Payee and choose the Owner Investment as the associated QB's Acct. If the owner takes cash out of the company, you would use the Owner Draw account. Each of these accounts will give you a clear record of what came in and what went out. Since they are both Sub Accts of the parent Equity Acct., that account will show the big picture.
The variables which may make you modify the above a bit is if there are multiple owners, if you show ownership as Stock vs. just and Equity Acct, etc. But to get the deposit into the books the above will work. Then just confirm with the Tax Accountant if you need to modify the transaction.