I am a S-Corp. I received a lump sum direct deposit for my entire per diem allowance for a project I completed. What category should I use? And how should I record it?

I'd be delighted to help you on how to record lump sum direct deposit for a project you completed, new2thisnew.
 

When we received payments, we can record it as bank deposit, and it should affect the Accounts Receivable (A/R). Here's how: 

1. Click the (+) New button and select Bank deposit.
2. Enter the Account and Date.
3. Under the Add funds to this deposit section, select these options:
   ·        Received From - customer's name.
   ·        Account - Accounts Receivable (A/R).
   ·        Amount - received payment
4. Fill-out the rest of the fields and then click Save and close.

Once we create a deposit and use Accounts Receivables as the affecting account, we'll have to link it to the project invoices. 

1. From the (+) New button, click Receive payment.
2. Enter the customer's name and the Payment date.
3. Mark a check on the Invoice to be linked.
4. At the Credit section, also select the Deposit.
5. Verify the Amount and then click Save and close.

For more details, please refer to this article: Record and make bank deposits in QuickBooks Online. 

Once we're all set, we might want to check out this link for reference in reconciling your account flawlessly: Reconcile an account in QuickBooks Online.

I'll be around if we need more help in recording lump sum direct deposit for a project. Please feel free to add them in your reply and I'll take care of it for you. Keep safe and have a great day ahead!