I am a software engineer living in California looking to invest in Omaha, Nebraska. 

You'll get access to their software system that analyses deals to estimate flip profit.AgencyOne: 100% commission, $50-100/mo + $10-200/transaction.Other low monthly fee brokerages: HomeSmart, Better Properties, probably even more.

Is there a software that would be good for apartments and self storage or should we look at two induvial software systems?

I use software for my invoicing judge completely ignored the invoice and allowed a taxpayer to redeem as if I had never responded.

If you are managing over 100 units, you should probably look into professional software.

I ran my numbers assuming I had a property manager but I'm leaning towards self managing via software and apps for the day to day stuff and seeing if the money saved is worth the hassle.

You can also buy lists from companies like list source and there are some REI software companies that have a cash buyer search feature.Some of best ways to find motivated sellers is to purchase lists from companies like listsource and or compile lists from city and county like 60-90-120 days late on mortgage, pre-foreclosure, delinquent taxes, water cutoff, code violation, probate, divorce, etc.

I am also looking into software like REIFAX for leads and I am on various wholesale lists as well as I am on Zillow looking for deals. 

Has anyone ever used or heard if Reonomy? Would you refer this product? Its pretty costly is it worth the investment?

I've been involved with startups for as long as I can remember - eventually landing myself in a fast growing recently IPO'ed startup in LA, working as a Product Manager for their software engineering team.