Some questions your lender could help you with: What is the Mortgage Insurance (MI) payment that is required if you had 1 loan at 90%. The rate on the first mortgage would likely be higher as well due to the added risk layer of being 90%. How does that payment of 1 loan compare to the combination of your first and second.
With 9% second, it sounds like a fixed rate loan, but you should confirm that.
The time that you expect to keep the loan is important. The lowest cost option, currently, is probably the way to go if you intend this loan to be short term.
A one loan option with MI may be more expensive at the moment, but it is a safer long term solution. To eliminate the second later would require a refinance, and of course rates cannot be predicted for that time, but the trends indicate we will have higher rates for some time to come. The refi would also include fees. Mortgage Insurance can be canceled once your loan balance hits a certain point (your lender could give you the specifics).
Options if you are eligible:
VA: WIth 10% down on a VA loan, the funding fee is reduced and there is no Monthly MI
FHA : There will be MI with an FHA loan and usually a 90% conventional loan is similar in payment to a 90% FHA loan, but the FHA product would allow you to put less down if you chose and keep some in your emergency fund.... more