You have our condolences. This is a tricky corner of the world of regulatory risk management and the only banking regulation with a death penalty (for your institution. Individuals only face 20-yr prison terms.)
If you research this heavily-discussed topic, you will run across the contrarian view that Phase II exemptions do not represent an acceptable cost/risk/reward ratio in many cases. You are not required to have exemptions, and for many customers with cash spikes it's cheaper to file the handful of CTRs each year than to set up and maintain an exemption.
Examiners crawl all over exemptions, and you'll certainly be cited for even the smallest infraction or oversight. Over the years, exemption errors have lead to some of the biggest penalty cases.
Unless the net savings (CTR filing cost minus cost of exemption administration) are substantial, a Phase II exemption trades a sizeable risk for an insignificant reward. Know your filing costs and weigh the alternatives carefully.
Good luck in your new job!