You would need to let them know you are 2nd lender and want to pay the loan off.

A lot of the owner occupy loans require you to live there for at least a year, so it's not forever. 

I would get an attorney or title company involved to create your loan documents to ensure they comply with the law and cover all the aspects you need.Another method that is likely your best bet to take on investors is to create a joint venture (JV).

And your point about a lingering HM loan makes sense.

Make sure you talk to a Banker or Loan officer that is well versed in both SE (Self Employed) income and also Non/QM programs.One tip I will give you as a Banker is open up a "Business Checking account" and for the next 12 months pay "Everything" out of that account. 

Doing a 75% 1st mortgage and 15% heloc or heloan would likely give you better cost of funds all around.If this is an investment property, you can do 80% cash out refi using NonQM loans such as DSCR loans, but at a higher cost/rate than if you stick with 75% loan to value. 

Quote from @Brittany Minocchi: I'm a bit farther north, but I've helped a couple of people with loans in that area - the properties seem to be working out well for them!  

Also, I am guessing that due to the state of the house, it would not qualify for a conventional loan?

I'm an engineering student planning to start a business after graduation.

I've been pre-approved for a bank loan but haven't thought about someone with experience working with investors for deals.