Grant Tracking through Fiscal Agent

We are a small NP that is expanding and trying to get our books into QB pro 08. We have received 2 grants so far - Grant A must be administered through a 3rd party fiscal agent, Grant B does not. Both are from the same funding agency. Both grants are strictly reimbursement basis. We have to buy or get invoiced before requesting that amount from the grant. The monthly procedure for Grant A is: 1. Person buys item; submits receipt to company treasurer 2. we submit to the fiscal agent a budget detail sheet requesting the funds we used, plus a % for them for grant administration. 3. Fiscal agent requests funds 4. Fiscal agent disperses by check all our direct costs, but keeps the % for grant admin. 5. Treasurer deposits check, then reimburses the person who bought the item. If we don't use it all, we don't get it all. Sometimes, on Grant A, if we buy something big or have a contract payment, we can give the vendor invoice directly to the fiscal agent and they will pay it for us instead of one of us paying from personal funds first. Grant B: 1. Person buys, submits invoice to company treasurer 2. Treasurer creates budget detail sheet for record keeping purposes, but submits request to funding agency directly. All costs are directly reimbursable (no admin fee, overhead, etc.) 3. Funding agency direct deposits funds into company checking account 4. Treasurer writes reimbursement check to purchaser. The granting agency has been quite clear that we need to track all the money, including the indirect fee that the fiscal agent charges. So far, I've been doing this with excel. My questions: 1. Who is the customer for Grant A, the fiscal agent (who gives us the checks drawn on their account) or the granting agency? 2. How do I handle bills that are given to us but paid directly by the fiscal agent? 3. Is it correct that all the money from Grant A that is distributed in our name to the fiscal agent is considered our income by the IRS? Or since some of it (stuff paid directly, % fiscal agent fee) never hits our books, maybe that's not considered income? And if that's the case, is there still a way to track all that is distributed in QB pro in the same company file as our regular books? I would really appreciate any help you can spare. -Payton