We are looking for a CPA that knows this field and knows software like QB and Expensify.

As for missing expenses....management software, management (regardless of if you are self managing), office supplies are a few that pop into mind.

If the tax accountant is using a software - it should be easy as clicking 1 button.

@Kyle Bergren , good point about having access to automated services and software.

There are a lot of PM software systems that allow you to bill and collect rent online.

This can be done with software which I can't mention here or this post will be flagged as spam (ha).

My recommendation is to search for a software that will assist you throughout your search for tenants.

Assuming this is just a plain vanilla rental, it should not be subject to self-employment tax, and it belongs on Schedule E, not Schedule C, where it sounds like your tax software is currently putting it. 

For anyone with fewer than 15 - 20 units, I don't think paid software is even necessary.

Use a software.