Hi, although I'm a neophyte, I'll try to tackle this one. After you file with FAFSA, your EFC (estimated financial contribution) is determined, and your financial aid office determines the amount of subsidized and unsubsidized Stafford loans you will be able to receive (in addition to any other grants, work-study, etc. that's available). Depending on the student budget (determined by your FAO), the Stafford loans offered may not be enough...that's where alternative loans come into play.
Stafford loans are easy to qualify for and have good interest rates and terms (government loan), while private loans typically have higher interest rates, origination fees, etc. Therefore, Staffords should be used to fulfill most of your financial need (that is, if you can't get tuition waivers, grants, scholarships, etc.) Moreoever, your credit-rating determines the type of terms a lender will be willing to give you for that private loan, i.e. the better your credit, the better the interest rate or up-front fees they'll offer.
My FAO recommended that if I needed to apply for an alternative loan to make up the difference between the student budget and my Staffords, I should try to use one lender to administer both. I think I'm going the MEDLOANS route...recommended by the AAMC and administered by Bank One. Do a search on the AAMC website for the MEDLOANS terms for their Stafford and ALP (alternative loan program) loans.
One more thing: all lenders are NOT created equal. Even though it's the same Stafford loan, some lenders pay the origination and guarantee fees for you, some give interest rate cuts after a certain number of on-time loan payments, others cash-back...it can get confusing when you are lender shopping. Take your time, read the fine print, and best of luck to you!!!