For me I divide the distance equally for the number of tenons I want to use and mark the centre lines, and at the start I used to do the common trick of all on one board tight, then on the other board first one tight then the rest loose, but as the domino tenons have a couple mm of play, I now pretty much do all the mortises on tight. If I'm just doing a single tenon in the joint I'll use the left or right hand side of the Domino plate as the reference. I find I very rarely use the flip stops on either my 500 or 700, and I think over the years I maybe used the cross stop once.
To make it easy and repeatable, I rarely deviate from the appropriate default height, and always reference from the top faces. Apart from customising the depth to cater for wide to narrow stock joining, keeping the settings basic make it pretty fool proof, and you don't have to remember "that particular" setting you used for a project.
I do take care to mark joins with A1-A1, B1-B1, etc to make assembly easy. Honestly, don't over think it, so long as you develop a habit and stick to it for handling the reference points, it just becomes so easy.
