If you setup your videofx via the ISBoxer in-game gui, (CTRL+ALT+SHIFT+G), then you can use the Import tab to import VideoFX settings between character sets/characters.
If you setup videofx via actions in your profile, then duplicating is easy, you just call your setup for the new character set (although if you've assigned targets to specific characters, excluding DXNothing, this usually wont work, normally it is better to assign to slots, although this becomes problematic too).
The issue comes about if you have something configured that does not apply to that character set because the class of the character in a specific slot dones't have something you have videofx'd. In these cases, you should be applying videofx to
Action Target Groups instead of slots, and maybe with an
advanced target to get the ordering. I use both of these for dealing with healers that are not always in the same slot and making sure certain classes have abilities display on the main's screen, and if a team does not have that class, then they don't display. This can add a little bit of work to figure out the details, but it turns out pretty good in the end.
I also virtualise the setup so a 3 man team runs a different layout to a 5 or 6 man team, because the locations are different. This is a PITA, because it means setting up certain parts more than once, but it turns out not a lot moves around because when running a stacked layout you fix the size. I just have a bit more black space on my dxnothing when running smaller teams so my main view does not change, and I don't have to figure out 30 different positions for videofx windows.
For showing/hiding videofx, I use a two stepped mapped key which runs a
videofx action to show/hide the videofx windows. I've separated the creating videofx to a mapped key which runs when my character set is loaded/reloaded (there is an option for this on your Character Set). Destroying videofx doesn't happen very often for me, but I do use it when switching windows for dragging certain party frame elements around because I can't pull them from the source and the viewer on the same window, so I need to grab them from a different characters frame. I make use of an
advanced target with select (#) to figure that out for me.
For keeping track, something like
large character names for each window. A menu works too, but for some reason people find clickbars easier to get their heads around. MiRai uses a menu with fancy rendered button images in his videos. I use boring text, so it ends up looking a bit flat, although recently I found some fancy images, but I use these as a right click popup selector...