Im looking to colour the edges of all the armada tokens. What types of permanent or paint markers work best? Will they protect/damage the cardboard? And what colours work best for armada tokens? Thanks much

Acrylic paint markers, available for 2 or 3 bucks at WalMart or a hobby store like Michael's or Hobby Lobby or JoAnne's Fabrics. Put on 3 or 4 coats to the token edges and they look really sharp. I'd estimate they protect the tokens a bit, it does change how they feel when handling and they sound different in the tackle box or when you drop them on the table.

I used a different color for each action so they are easy to differentiate at a glance. For defense tokens I used a bright neon/lime green.

I also play X-Wing and Star Trek Attack Wing. I've paint markered a few X-wing tokens and all of my Star Trek cardboard, using different colors for each faction (about a dozen factions in STAW!) That's ship bases, maneuver dials, and color coded action tokens. They all look great.

Yep, paint pens though mine are oil based. I haven't seen acrylics. At any rate, pick a color that complements or matches the token. I use gold on command tokens, blue on defense tokens, black for imperials and obstacles, neon blue and neon orange for the speed dials, silver for rebels, and yellow for objectives. I could go on but you get the idea. They might protect a little but not much.