The goal of panel design is to optimize assay resolution by creating bright positive populations while minimizing spreading of the negatives (see also compensation controls and FMO controls).
Know your instrument’s optical configuration and fluorophore spectra
Divide fluorophores across multiple lasers and distant emission ranges
Put bright fluorophores on rare cells/low expression markers, dim fluorophores on abundant cells/highly expressed markers
Put high spillover fluorophores on mutually exclusive markers
Use a single dump channel to exclude undesired populations