That is really up to the contract, most times I see the PM collect this "for their extra bookkeeping".

I plan on having 50 units by the end of the year..what's the best/most simple software to use for bookkeeping?

Sounds like you might want to think about farming out your bookkeeping both for last year and the future.  

Odesk for bookkeeping may be a solution I need, entering receipts is so tedious.

Payroll, bookkeeping, etc can mostly be done remotely.Here is a great list of questions to ask a potential accountant:http://www.biggerpockets.com/forums/51/topics/70447-questions-to-ask-a-cpaAlso check out the www.NAEA.org page in your search.

Right now, we're thinking that my husband does the project management and I do the design, bookkeeping and deal analyst.

you did not include in your expenses1- vacancy expense2- leasing fees (to broker)3- property management4- repairs5- bookkeeping, accounting, tax prep6- depreciation reserve (limited since the HOA should have its own reserve)Big issue is financial condition of the HOA.  

I'm no accountant, but I've flagged 20-40 questionable bookkeeping items in the last 6 months.

The longest I remember which is what all my transaction records is 7 years, there are 1 year and 3 years, but I told my bookkeeper to keep everything for 8 years (except those that need to keep permanent like incorporating papers, EIN filings, etc) to be on the safe side.

If you have a bookkeeper and is OK taking that extra cost, it works, but for me, I want it just like Quickbooks, where I download and tag the transactions and done.3- I found that their online leasing workflow to be top notch.