I was told by my lender that this has to be my primary residence for some time.  

Then, you need to study the IRS Publication 523 regarding the Sale of a Residence.

My plan is to use my HELOC from my current primary residence as the down payment.

Keeping LP's in the dark is an art and science.

Investment Info:Single-family residence fix & flip investment in Charleston.

MTRs do have higher turnover than a typical LTR (usually between 2-4 times a year), but since most MTR residents treat the space well and since there is less moving in and out of furniture, it is not uncommon for an MTR to actually have less wear and tear over the year than an LTR (and a lot less than an STR), Arbitrage for the MTR operator has its own sets of pros and cons, but I just wanted to address the question of why would a property owner ever want to allow an MTR in their unit. 

What that means is you can stay in your residence and I will be taking over the garage (the property will be split at x point??)

You could 1031 out of the property, purchase a new one or something you might like, "Live" there for two years and convert the property to a primary residence. 

These are among our favorite residents to host.

Primary residence capital gain $250,000 exclusion.