State Tax Filing Headache : Work in one state. Drivers License in another

Alright folks, so here is the situation...

 

I work in MN and I reside there roughly about half of the year, the remainder is in Iowa.

In prior years I have done my filing thru the State of MN, I thought I would change it this year because of my dads house, the LLC, and well it just made sense.  However, when I did this, right away it said I owed over 8K in taxes.    When I went back to change my residency to partial, it was changed to zero.

 

My paystub reflects state of MN.

I have a drivers license in Iowa

I have an established LLC in Iowa

I am helping my dad with his mortgage for his house and am a co-borrrower on that in Iowa.

 

My questions----

1.  How should I be filing?

2.  Why did the system say my balance was over 8k in the negative? 

3.  How should I fix this?  Should I have been reporting my taxes differently in past filings?

 

Thank you!