However I feel like we are missing out on tax deductions for the business, since those transactions are not being made from the business’s account.

When analyzing rental rates, vacancy rates, property taxes, and other financial metrics, it's important to consider various factors.

My CPA advised me to split the generic costs such as property tax and water bills equally between both units, which seems reasonable.

Is your DSCR ratio greater than 1-meaning are you cash flowing (according to the lender's criteria of mortgage, property taxes and insurance (and HOA) if applicable).

I smell a refi in your pipeline a year or so from now, remember this isn't a home loan, so "two years of tax returns showing a profit" is NOT a hard/fast rule at all to get the best terms.

While we do not see income from these properties and are not managing them we do have a significant amount of depreciation and losses that have been assigned to us and carried over from the past couple years.I am invested in some growth/equity focused projects already and am specifically looking in reliable income focused strategies that are tax efficient provided the losses I have from my family.

This loan type looks at the rent currently generated by the property OR the anticipated market rents (determined by the appraiser) and compares it to the monthly principal, interest, taxes, insurance and HOA (if applicable).

there are many tax complications?

The Bank send a 1099 for the charge off for this Tax year. 

Prior to speaking with an attorney you need to learn how the syndication model works.Underwriting, LP/GP structure, fees, etc.A great book is Best Ever Apartment Syndication - textbook for this business.Happy to provide more insight on the process, if you want to send me a DM.