Through out the year we are sending out receipts as gift come in. But for our employees that make a monthly donation per payroll they only want a reciept at the end of the year. How do you do this procedure? Do you use a recurring gift batch? Do you have to go into their record (Bio2 taband change their receipt to once a year also or is that not needed?

Aren't they getting tax receipts from your payroll?
It should be reflected on their form for income tax.
Or if you're printing receipts in-house use recurring gift, mark them "consolidated" on Bio2 and send a receipt for last calendar year.