the commands...you want the one for marking.
https://github.com/webbukkit/dynmap/wiki/Commands
and the different icons
https://github.com/webbukkit/dynmap/wiki/Using-markers
so example for a portal you go
/dmarker add <label> icon:<icon> set:<set-id>
/dmarker add Blues-portal icon:portal set:Portals
labels = name to show on map
icon = the image on the map
set= what filter it falls under so a portal is a portal. you can see what filters the map by viewing that layer tab on the map page in the upper left corner
also the POT filter/set means point of interest
to do a territory like i did for my mtn
go to a corner/edge were you want it to cover and type
/dmarker addcorner
keep repeating this till you almost surrounded your territory
and if can please try and keep under 20 corners
when at last spot type
/dmarker addarea <label/name>
Ps please dont link map on board. dont want an overload of view