Not exactly sure what's going on, so let's just review Accounts and Invoicing in general.
First, I'd suggest you rename your Misc. Other to Travel. Or if you already have a Travel Acct, use it.
So now to how these items are in your Checking and how you Invoice.
At the top of the QB's window Click Lists and then Item List. Do you have your various Services and a Mileage entry in there? If not you should. I have various Consulting Items based on if I do work in NYC, NYS or Out of State. Names are all abbreviated because only you see them and give some thought to the name so as you type they will come up quickly.
Then when you Invoice you pick these Items, change the Qty - could be hours, miles, number of 2x4s or whatever the Item is. Description will fill in with whatever you originally put in, but you can change it. Same with the default price, change as needed.
When you get a Payment, you go to Customer in the top menu and Receive Payments (you can also do this through the Customer Center or other ways) and you enter the Payment and match it to an Invoice for that Customer.
Now the Deposit... This messes up a lot of people. Whether you get a Check, Cash or Direct Deposit, you enter the Payment as above. But in QBs this does not show it IN your CHECKING, it is in the Undeposited Funds Acct. The reason for this is you may get a check on Monday, but not deposit it until Friday (old school before you could use your phone) so QBs is set up to make sure you show the actual deposit date so QBs will match your Bank Statement and it makes it easier to match.
This also gives you the option to show multiple checks as one Deposit, which is also more in keeping with how you actually make deposits.
So.... You get the Payment, you apply it to the Customer, then you go to Banking menu and Make Deposit. Then you individually check off the pending Deposits or you check multiple deposits all depending up on how you are actually going to deposit them in the bank. Select which Bank Account if you have more than one.
So now in your Checking you should show Deposits on the days you made them coming from your Undeposited Funds Acct. And if you go to your Customers or the Invoices, you will see the payments.
But what you should NOT see is the individual Mileage or any other Service or Item you've invoiced for directly in the Checking Acct. Only time I could see this would be if someone Reimbursed you for Mileage in Cash and you made a deposit of the Cash. Bur I doubt your Accountant would like it done that way.
So go back and look at how you entered the Items/Services/Whatever in you Invoice and how those items got directly into your Checking. I'm going to guess they were just set up wrong and getting applied to Checking when they should be applied to a Mileage Acct or some other Expense Acct. So a quick change of the Account will apply them to the correct place.
