Yes, that is similar to the way I do it. I put departure time and station, train name and number and arrival station all on one line, for each train leg. As each is called up on the computer, I ask for window or aisle and preferred side (ie "Fuji-san side," etc.) I always hand them my Rail Pass first, then proceed with specific requests.

Most major JR stations will have at least some agents who speak English but even those appreciate having the specific trains written out as it is easier to read than to hear and understand. I have had them see me looking at my itinerary and ask if they could look at it while they look up the trains. I just fold it so that day's trains are displayed and hand it over. They give it back with my Rail Pass.

There is no guarantee you will get everything you desire. The trains tend to be pretty busy. But making reservations a day or so in advance will definitely help.

Since I am a "belt and suspenders" type of guy, I often have a separate sheet printed up with alternatives in case my first choice of trains is not available. I've only needed that once, when I inadvertently arrived on a national holiday and my planned train was completely full. The second choice had a few seats left so I was only 45 minutes or so later arriving at my overnight stopover. That is unlikely to happen on the vast majority of days but it can happen.