Hi Yggdrasil,
1 & 2 have the same answer. When you create your NPCs, give each an appropriate "Key" string, which can then be searched by typing in a substring into the "Key" input field. This allows you to choose just the NPCs you need for each encounter. For example, if you have 4 NPCs in encounter #1, perhaps choose "E1" as the Key for each of those NPCs, then search for "E1" to just show those NPCs.
3. Initiative in Minion can be sequenced multiple times. This allows for any type of round sequence. So if you have a separate phase for Spells, then Archery, etc. just cycle through the initiative sequence multiple times, skipping characters that don't act during that particular phase.