I can assure you the vendor HATES this - as they aren't geared for taking in indivual checks. Requires manual processing. If the client is "influential" enough, they may accommodate that - but as you point out the problem is the records (recordkeeping and payroll) can get out of sync. The recordkeepers I've worked for prefer the employer to take the checks and remit the money as part of the normal payroll feed-contribution deposit.