I live in Onondaga County which I believe has a similar system to yours, and I own a 996P2, 325P2, and the SDS100. I think the only real adjustment the 996/325 have is the P25 Threshold setting. Also keep in mind physical location, and antenna type can help as well.
I wanted my 996 on my nightstand next to my bed, and played around with different antenna hook ups until I finally found one that works pretty good - an old telescoping HT antenna I bought at a hamfest. Not saying it's perfect - the SDS100 definitely out performs it - but I'm happy enough with how it compares to the SDS.
Play around with the threshold setting, location, and antenna types/lengths and you might find a combination that works reasonably well. The 996 is a great scanner, but not an end all solution for LSM systems.