The IRS offers no relief provision for S-corp shareholders who fail to take reasonable comp.  I think by probably should.  So the only correct way, is to file late payroll tax returns.

Given the harsh penalties associated with that I have seen several other tax prepares use the following methods:

1) book it as a loan

2) book it as if paid on a 1099-Misc, subject to SE tax

3) Ignore, with or without stern lecture.