In fact, in many cases, you don't have to payoff one before you use it again for another property, as long as you meet the owner occupied requirements. 

I am looking to owner occupy for 1-2years, then rent out both units.  

You're not going to find lenders to do non owner occupied deals at 90%.

Because my home is owner occupied, I was able to do a conventional loan with MIP at 4% down.

One unit is vacant (that will be occupied by me) and the other unit has a renter whose lease is up in Sept/30.I do not wish no renew the lease for this renter as I'd like to make some renovations on that unit before renting it out again.

They are all occupied so I think selling them myself on zillow, etc, may not be great because I can't be there to show them and I don't want to disturb the tenants.

Here are some things that I want to do, but I want to get your opinion and any other ideas- charge a flat rate for each unit each month, and obviously this would be written in the lease and tenants would know ahead of time- charge a rate by sqft, so tenants occupying 750 sqft pays less than 1000 sqft unit, rate is FIXED and known at signing- charge a rate by sqft, so tenants occupying 750 sqft pays less than 1000 sqft unit, rate is VARIABLE and is calculated from actual water bill- increase rent price?

It seems like a great idea to get a HELOC on your property ( if it has equity) while its still owner occupied, you will have funds available when you find your next deal.

Or is it better to hit a neighborhood you like and just filter for equity and owner occupied in PropStream?

If you are not occupying the home during the application process is will be considered a rental/NOO - Non owner occupied home.