If you have two Sniffers, by all means have one at the client and one at the server for comparison. Otherwise, move back and forth between the client and server. If the response time is fast next to server, but slow to the client, the latency is being induced by the network. If slow sniffing by the server, it is the application (or the server itself), especially easy to "prove" if there is a tcp ack and then much later, the response is sent.
You are right, you will have to match C/R pairs in the decode tab to look at delta times. Using ART will make this infinitely easier. I would look at average response time though, vs. the 90%. That is just personal preference. I like to see the whole picture. If the port number of the application is not a "well known" you can always add it in Tools, Options, Protocols, and then to ART's properties. Life is different in BettyLand