To get the little unit icon appearing in the intro text you need to set a protagonist for the scenario, and be currently playing that side before you save the position as a scenario file. Obviously this won't work for scenarios with the barbarians as protagonists, or where there are no objective points as victory conditions. Secondly you need to have an example of the unit you wish to appear in the text box currently selected when you save.
For an example: a WW2 scenario with the Germans as protagonists. I choose to have the human side as the Germans via the cheat menu, and then select a tank unit. I then save the scenario file. When you begin the scenario that tank icon will appear in the intro text.
As for graphics programs, I use a registered version of Paint Shop Pro. All the unit graphics are stored in the units.gif file, and you want to be able to cut and paste into this without changing the palette. PSP allows you to save the default palette so you can then apply it to any artwork you create later on.
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