My suggestion would be to purchase 4 paint pens They should be between $3 and $5 each. You'll want blue, green, red, and pick another bright color that will stand out...say purple or orange. These are to paint the sides of your cardboard items. Blue is for your blue tokens: shields & cloak. Green is for focus, evade, reinforce. Red is for crit, stress, ion tokens. Use the 4th color for the sides of your maneuver templates and, if you want, your bomb/mine tokens. That will make everything stand out more on your black background. Oh, and for target locks, I like the idea of blacking out one side.
I personally love my acrylic upgrades and highly suggest saving money for them. You can get some nice ones for reasonable prices. I use Daft Concepts for my general play tokens and target locks and use Cog-o-two for my maneuver templates. My suggestion would be before getting acrylic, pick up a play surface you're happy with. Do some research and find something that appeals to you that others have said work well. I use a cloth mat from Corsec Engineering...but that was expensive and probably not a good fit for your situation.