@sharieb 

Make sure you have separate liability accounts for each payment that will come out of your bank account - FUTA, SUI, Fed Withholding, 401(k), health ins., etc.  Then, make sure to assign the proper liability account to the payments made: health ins. liability to your health ins. provider payment, SUI to your state unemployment agency payment, etc.

As far as accruing vacation compensation, that is an in-depth discussion and is probably best handled by the NFP's CPA.  IMO, if your NFP needs to accrue vacation expenses, then you need a good accountant.  Accruing vacation is a GAAP requirement but the tax treatment is different.