Anyone with USDA Housing? Question on rent Collection

Have a question on rent collection for those with USDA-RD housing. Does RD allow you to apply the rent collected to a past due balance or other fees first. Thus leaving the current month's rent due? Or do you have to apply it to the current month's rent? I thought I saw in the 2-3560 somewhere that we have to apply any payment to current rent first, but now I can't find where. Thanks for your help all!

Your question is very interesting! We have a Section 515 property which is fully under USDA-RD, each unit has RA on it. Oddly, this has never been a problem in 14 years for us. We have a policy through the management company that does not allow past due rents under RD. Now it may have happened, and the management company dealt with it on a deficit with RD, but I would have known about it, and quickly and loudly!
Our policy is "Due on the first, late after the 10th(late charge applies), and "Get boxes after the 15th, because you are moving". However, my memory serves me to think no one here has ever been later than the 12th on paying their tenant contribution. Speaking off the cuff, and considering my management company, I would say the rent paid has to apply to the current amount due, as their would not/should not be any amounts past due. Anymore, Management Company won't accept a check for the wrong amount these days, as the computer vomits out a nasty gram on errors. (Over and Short Report).
I have, however, been involved in RD's recovery of rental assistance. In this case the RD regional office serving us would contact the management company, and set up a repayment plan for the tenant, in the case of paid out RA that was overage due to errors in reporting income. When RD says they will recoup the money, you can believe them wholeheartedly.
I have said a lot but have not answered your question.

Edit: I do remember a few years back, a tenant was in the hospital, then to a nursing home for a time, and it was about 45 days before a family member came and caught up the due rent, but that was all legitimate and due to circumstances beyond her control.

I live in a subsidized rental property in NJ.The USDA pays some,i pay some.In Dec of 2013 i paid my rent,$530.00,the USDA paid the rest.The mgt company claims i still owed $20.00 for some reason?Now its Jan and i paid my entire rent again on the 10th of Jan because we have a 10 day grace period.
But now,because i owed $20.00,the mgt company says im 2 months behind in rent,therefore in violation of their rules.They claim the USDA changed its policy and anyone whos 61 days late in rent can be evicted?So they are saying i am owe the 20.00 for Dec and didnt include it in Jan rent so im in arrears 60 days?Today i went to office and paid the 20.00.
Can they still evict me or since im fully paid,they cant?
I have 2 small children im raising.
Would a judge allow this?