How do I deal with an unorganized customer who hasn't paid in months?

I run a business with my boyfriend and lately were having major problems with one customer in particular. We manufacture as a service and are required to purchase all the raw materials for this customers products. Now in the beginning we had problems because I use Quickbooks and for some reason a few invoices were doubled. This customers current balance is $40,000.00 of which half is paid to raw materials and half to labor (which we have already been paying from our own pockets to our contractors). Now hes been doing his accounts which have stretched back until last year and claims that WE owe him close to $5000.00 paid through double invoices????? He clearly has 40,000 outstanding but claims that hes paid it all when he has not. Im so petrified that the company will just go into bankruptsy and we'll lose everything. What do I do??

You just need to pay someone to audit your books. Once you have the evidence that money is owed, you can send your customer a bill stating that if it is not paid by _____* you put in the date*, court action will proceed. Or you can send them to collection (unfortunately this way you will need to give a percentage to the agency - BUT IT IS BETTER THAN NOTHING!!!) Bankruptsy is a last resort. Hire a numbers person and breathe.
Stay strong and persevere. Success always takes hard work, but it is worth it :)

Hire a CPA to review your accounts.

COURT ACTION FTW... YOUR CLIENT IS BEING RETARDED

Two words: Hit man.

why don't you get your accountant to check your book (quickbooks entry) once all the figure is right, sent the invoice to your client with the correct figure and if they still insist that they already paid it ask them to send prove of payment (ie cheque number or EFT receipt number/date/amount, etc so you can track it).

make sure your book is correct first (there is no double invoices) and get all the record of all your customer payment so you know which invoice has been paid and which one is still outstanding so you are in stronger ground to move a head to claim the missing payment and if they still don't want to pay I would suggest seek legal advice.

Hope it help and good luck.

Cheers