Hi Richard,
Yes, it is a manual process for cheques.
In PayDirt's help file:
To turn on the option to track cheque numbers go to the Setup -> Company Settings -> General Options -> Payroll Batch Options tab and turn on the checkbox that says "Remember Starting Cheque Number For Batches".
Note: you would normally only do this if you have separate cheques for payables and payroll. If instead, payables and payroll are sharing the same stack of cheques (and cheque numbers) it is better to leave this option off so that you don't accidentally use cheque numbers in payroll that have already been printed in payables.
If it's an issue you don't want to deal with, you can set up to use blank cheque stock in both AP and Payroll and have different number series in both. Or just isolate a box of your pre-printed cheques for Payroll only so AP doesn't mix in.
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Dan Desautels
DezTek Solutions Inc.
Thunder Bay, ON