I am not sure on the SE with the Honda CB, my guess is that it is at the back of the radio itself, pull off the small storage tray above it and look down there and see if you can see it??
I wouldn't expect a connection under the seat
I have a Aspencade, so have a J&M CB installed, when I installed it, I put a connection in the trunk to make it easy to check the SWR.
May find someone else here that can tell you where the SE has that connection
Take a look at THIS and THIS. Even though it shows the 1800, the 1500 is similar. On the 1800, there is no choice but to check using connector right by the antenna. It only uses a short amount of coax so it isn't a big deal. However, usually when checking swr, there will be a longer length of coax and that will play into setting the swr. You will want to use the full length of the coax for tuning the antenna and hook up the swr meter to the end of that coax. On Aspencades using the Hondaline CB, the coax is a separate cable that attaches to the back of the CB and then to a connector hooked up to the antenna. On the SE, IIRC, this coax is part of the main wiring harness. However, there still should be a gray connector under the seat near the base of the antenna and also another plugged into the CB. That part of the coax that plugs into the CB is where you want to check and fully tune the antenna.