So how did you divide job between minions?
having only 100 minions is not much. Workers are fairly useless except when building stuff. but doing missions or protecting the base they are worthless.
so:
10 workers
5 of each middle level
10 of each top level.
that allows me to take out a single or double attack from soldiers (with henchmen help) and the army of diplomats and playboys protect my base from tourists, non-violent agents (thieves, investigators etc) and super agents...
i adjust that when i need more minions of one kind for a mission.
the drawback is that everything takes forever to build. especially in the beginning of second island which took quite long time to have everything set up (especially since i am playing with one entrance)
your ideas?

I usually allocate 10 workers and 10 of every mid-level minion, with 5 of each top level minion. This tends to provide the necessary minions to carry out most acts of infamy without having to reallocate my minions' jobs. I personally haven't found minions particularly useful for dealing with violent agents, and typically deal with groups of soldiers by just bum rushing them with 3-4 henchmen (making sure all the henchmen get to them nearly simultaneously, then having Jubei teleport in just before the other henchmen arrive so they can close the last bit of ground without taking fire).

soldiers and veterans are dealt by my henchmen who attack them when they get close or violent on my workers. rest of the agents aka the majority are dealt with social workers. sometimes a single or a couple of agents will go through my security door but i always have a four dot security door next to the entrance allowing my henchmen to be always available to kill intruders.