this is what each editor does:
classic mode: place nearly all units anywhere and has extra ai scripts(bascially a more advanced staredit)
p12 mode: i would recommend starforge or scm draft over this but it allows you to place neutral units
base mode: preferred for terrain and i dont think you can place units anywhere
alternative mode: i think i remember that addons can be placed anywhere in this mode.
special mode: units take up 1 pixel space so you can "stack units"
dont forget that these editors share a lot of features
Straight from the ReadMe you get...
CLASSIC-MODE:
Standard version (All scripts, standard unit-setting, buildings everywhere (Standard Emerald)) - Buildings can be placed totally independent from terrain.
P12-MODE:
For the neutral player 12 (Ale scripts, all units for player 1-8, building placing like in StarEdit).
All units are given to player 12 when starting this mode, so this mode should be used at the start of a project to avoid annoing corrections with another mode later.
BASE-MODE:
For the fundamental map designing (StarEdit building placing, everything for player 1-8, also critters)
ALTERNATIVE-MODE:
An alternative to the Classic Mode (Addons are independend and placable everywhere) (Critters for player 1-8, the most other things are like the Classic Mode)
SPECIAL-MODE:
Good for RPGs and special projects: Every unit/building requires just one point on the map, so e.g. buildings could be placed in another and above each other. (Addons and critters are not neutral, the Addons must be placed like buildings in StarEdit.) This mode should - if necessesary - used at the end of project to make it perfect.