The substantive tests would be the same as
large audits (i.e. cash recons, search for unrecorded liabilities, fixed
asset additions, etc.)  The difference is, because you cannot rely on
the controls of these companies, the ROSM must be placed at high. 
This will lead to larger sample sizes.  The documentation would be an
excel spreadsheet illustrating the sampled items you reviewed and a
memo with a purpose, procedures, and conclusion. 

I worked at KPMG for 4 years prior to joining the smaller firm where
I am now.  Small audits are actually easier (in my opinion) than larger
ones because there is not as much activity and the accounting is not
as complex.  if you can audit a large company, you can audit a small
one.