I mean in-game function, like when you've already pressed Ctrl+K and have tweaked with rival factions a little bit. The problem is, I can't, say, place supply pods or elevations, although it seems to be basic function of the editor. I click with my mouse at different locations and press 1 or 2, but nothing changes. Am I doing something wrong?

In Scenario Editor menu I can't do that as well, although there is a menu (in place of regular message panel) with number of options, including elevations and other object.

You have to select change elevations in the menue

Then you have to place the cursor on the tile you want to change the elevation.

Then you have to press right and left mouse button i think to go up and down

No.... its the enter key i think, and it only raises or lowers based on the menue selection

The random map generator in SMAC has some bad habits that the editor is essential to correct...

It loves to leave large land masses untouched while putting some starting locations on tiny islands or too close to each other.

So you can use the map editor to make sure all the races get a reasonable map and make sure large areas don't go to waste.

I also like to throw monsoon jungles under the factions i want to boost..... lets say i want the progenitor to be extra strong - monsoon jungle for them! you can use multiple monsoon jungles on the one map.