Hey Reklar,
Llama is right about the militia, the green ones are "recruits", the blue ones are "regular". You can get dark blue ones that are "veteran", but only from combat experience (eg someone has to attack their sector).
Once you trainers have totally trained as many green militia as you can (20 in each sector of the town - Drassen has 3 sectors, so max milita for Drassen is 60), they start upgrading the green militia to blue militia.
Its not terribly important to sweep the surrounding area of troops, unless you want the experience or potential loot. Its possible you might have a compelling strategic reason to do so - eg you want to move your main merc squad a bit away from the town, but you are not confident your current amount of Militia can defend the town. If you wipe out any surrounding squads, there is nothing to actually attack the town. Generally though, so long as you are confident your Milita can handle it, just sit back and wait for them to attack.
I usually find that if you train up to max green militia (20 in each sector), its safe to leave the town to defend itself, and move your main merc battle group on. Still leave some specialist trainers behind though, to build up some blue militia. Flo from MERC is good at training militia to start with, and quickly can get to be fantastic, expecially if you keep her for a while. Ira also becomes very good.
As for towns - more sectors does equal some more hardness, as obviously it is more battles you need to win.
BUT - the difficulty is mostly determined by the "character" of the town. Chitzena is a sleepy little tourist town, that people used to take their summer holidays at. Accordingly, the garrison there is pretty sleepy. Your only difficulty with Chitzena is getting there - expect to fight a few patrols on the way. Once Chitzena is taken, it is rarely counter attacked as well, given its out of the way location. San Mona is also on the way, which you should spend a little time exploring. Its the New Reno of Arulco ;-). The main shopkeeper of the game (other than Bobby Ray's) resides there.
As for Alma - well, its the headquarters and main training ground of the Army! So accordingly, there is lots of , well, Army there ;-). Going straight to Alma after Drassen is doable - but its a very "hardcore" option. The garrison at Alma is well equiped with Rifles and Assault Rifles. Its the hardcore option as assaulting Alma lets you capture these Assault Rifles for your own use very quickly, which dramatically increases your power.
So chtizena is much easier than alma - but also less rewarding. When you are on the mine screen on the strategic map, you click on each mine (might be right click) and see how much each mine produces - some are more valuable than others. Generally the Chitzena mine is the poorest - but it is reandom, so chitzena might be valuable in your game.