Well I use 1 pixel every time. And I do like the fact that when I create a new hull type SlotModder remembers it. It saved A LOT of type when I added a CPU slot type to The People's Mod.
The key is consistency.
As long as you keep it the same, the autodetect will work.
Another handy old function is the "lock slots" checkbox.
It allows you to click around to view the slots without worrying about accidentally moving them around