Yes, you can get on MLS by using a flat fee FSBO service. 

I'll be hiring a flat-fee agency to sell my home.

There will be a rise of flat fee brokerages (offering limited services) and creative compensation arrangements, such as RE consultants for time or a specific transaction.

Alternatively, you could do a flat fee for one or both units.

All I know is I'm just looking for strategy help/expertise and not for a company to manage my investments/funds who preferably charges a flat fee vs a % of my assets.

Yes people buy them and then move away and rent it out but their cash flow is flat, negative or barely positive because again, they're not rentals.Plus HOA hit you with fees for renting out your unit, annual paperwork fees...they're a headache.

I also pay for utilities for two units since they are not on separate meters.My additional question is: can I/should I raise the rents the $75-100 I would like to, ask for a pet rent, possibly ask for a pet deposit, and then also charge a flat fee for utilities for the 2 units I pay electric and gas for?

Flat roofs, old roof age, old electrical, cast iron plumbing and non impact openings will mean much higher premiums. 

There are some discount brokerages where you pay flat fee for a listing on the MLS. 

I assume you're paying the owner a flat monthly rent, but how do you handle the renovations?