Top and bottom have to work in harmony because they are not totally independent. But I guess I do prefer to get my low end dialed in first as long as I know my top end is an hour or so on the rich side. If you start with your low end first with the top too lean, your low end will be a little too rich and your likely to have a 2 stage idle (you will hear the carb clearing out excess fuel and then get back to steady idle). If you start with the top overly rich, then you will likely lean out the bottom too much to get more power on the bottom. This will usually cause a high idle and high operating temps. Of course this all assumes that you warmed up your engine and got everything heat soaked prior to tuning.

In any case, with these engines once you have a good tune, you are never more than a couple hours away from a perfect tune on any given day.