one check for multiple customers

I have a question...
I do landscape maint. work at two franchise stores in town that are owned by the same person. He requires that when I do the work, I give him two bills,
one for each location. So I set up two customers in my customer list. Problem is, when he pays me, I get one check for the combined amount. Is there any way that I can "recieve" one check and apply it to multiple customers? What I did this time was "recieve" the check for each store but put in the amount of the invoice rather than the check for each. This works to a point, but it throws off my deposit tickets in that I show a two entries on the ticket when really there is only one check. Any thoughts on another way to do this?
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One method - make the 2 stores "Jobs" of a single customer. You can receive a single payment for the customer and apply it to multiple jobs.
Another method - just use one customer/job. When invoicing the other store, change the address (either Bill To or Ship To).
Third method, using separate customers - Receive the full payment for one customer, then transfer the unapplied portion to the other customer. I won't go into details unless you ask, because I think the first 2 methods are simpler.
Fourth method - what you did, but didn't like.

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James Stewart wrote:

And this is a problem how? This happens here at least once or twice a month. When I have two amounts comprising one check, I draw a circle around the two, write "1 check" on the deposit summary, and re-write the number of items in the deposit. People at your bank get paid big bucks to sort out this kind of thing.

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