I think when the furnace is on bills skyrocket, so im thinking the size (possibly) though it does not seem small, and the duct layout have a lot to do with it as it is a 1925 all brick home, with new windows.  

Zillow I don't believe provides you ability to transfer their code/ layout into another website.

To me, it seems like it would make more sense to get a fourplex (higher cash flow potential and spreads the risk in case of vacancy), but so far, the Duplexes seem to be a lot nicer, a bit better fixed up, and have better layouts {ie. dual garages}.

What should I expect to pay for 10x10 layout?

It seems a lot more intuitive and user friendly than the other one. 

But I recommend you clearly lay out everything you need for potential agents, get their commitment on it, then bring it up if they are not meeting your expectations.

I use quickbooks for my rental company and they have an online payment system called IPN ( Intuit Payment Network).

NOT a great layout idea!

I know that it isn't that hard to create a 3/2 out of a 4/2; is this worth the time and effort along with the money to change the layout of a rental for a better marketing strategy?

It was ok but I have actually found QB more intuitive for me and switched to QB online.