Well I've worked out that is you are entering Switzerland from the north on the E35, that is actually the German A5 crossing at Weil am Rhine, Germany, one of the busiest crossings anywhere. Move your street view - if Google in Germany is allowed to - north a few km to Weil am Rhine and look for Zollamt Weil am Rhine.
What is there is, after the long queues (follow the icon of the automobile as you wind along past the queues of the trucks) a gray building you drive up to and wind around and get in the proper queue for either with Vignette or no Vignette - clearly marked - and if you are in the correct lane and displaying the Vignette correctly you will be waved through unless they are checking customs or immigration that day.
If you are in the no Vignette lane you will be stopped by a border guard and pay your CHF40 or Euro equivalent and the guard will apply the Vignette correctly. Unless they are checking immigration or customs that day they will then wave you on your way.
Just a few feet after you start, there is a parking lot, a filling station, a tasty Moevenpick Marché (slightly different format than other Marché) and other amenities of a rest area.
When you actually cross the border, as you say, it is a non-event.
If you are talking about the southern entry from the Italian A9 autostrada north of Milano, the crossing is at Chiasso, and similar arrangements apply, except the winding around is even more complex and erratic. You can get your Vignette there too.
Which way are you going?