I Need to Apply Two Manual Checks Against a Single Voucher. After I Entered the First Manual Check and Saved, I Could Not See the Voucher and Apply the Second Manual Check.

After you save the record, Query the Pay Vendor; the voucher displays in the Open Vouchers table. You can then apply the second check.

One of our vendors has directly debited our bank account to receive their payment. How should we record this payment?

You can record this transaction here, on the Manage Manual Checks screen.

I Cut a Manual Check for an Invoice. I Used the Check Tab of the Manage Accounts Payable Vouchers Screen to Record the Check. After Posting, I Realized that I Had Entered the Wrong Check Amount, So I Voided the Check. How Can I Use the Same Check Number?

After you void the check, complete the Manage Manual Checks screen and use the same check number but with a different check date.