Welcome to Xlights/NC.
There is no need to worry about universes. Yes your items in your display will overlap universes. Have you decided what controller your going to use for your smart RGBs? A F16v2 controller will let you have different strings lengths per output. Also 680 nodes, 2040 channels, 4 universes per output. That's using the 16 output controller. Now if you also get the daughter board, adding another 16 outputs, 32 total the numbers/nodes channels are cut in half per outputs. But the overall totals for the controller remane the same. The E682 controller also has 16 outputs but grouped in 4s. That means if you use all 4 outputs in that group, they need to be the same in type and length. Only a total of 3570 channels. Other controllers I'm not sure about.