Some thoughts and basic strategies for you:
Can you hit the Alpha ramp from both flippers consistently?
Can you backhand the Alpha ramp? From a cradle you should be able to hit this shot consistently, on the move its a little more difficult.
Can you backhand the spinner?
Can you backhand the away team shot? This shot is tough for me, so I don't use it too often, but maybe you can.
Are you using dead flipper passes to slow down the game?
Are you spelling TREK and Beam Me Up? I do this like crazy, and by the end of my games my spinner is generally worth some real good points.
When the ball is in the pops, do you know which lane the ball generally goes to? On my pin the ball definitely goes through the Up lane the most, followed by Beam, Me is last. It's good to know so you can adjust ahead of time.
What is your shooting the Vengeance plan? I try and not ever shoot from the left flipper when the drop is up.
Some Multi Ball related things:
Are you making sure you start a mode before getting a mb?
Some modes I like for mb:
PD1. The way PD1 works is, every shot is lit. Once you hit them, the shot is not lit anymore until there are only 2 remaining shots left, at which point everything lights up again. This lends itself to mb very well, as you can generally just try and keep the balls alive and you'll more often than not have a lit mode shot to shoot for. Additionally, the galactic mode is great for mb. During it, Beam/Me/Up are lit as well as the spinner and the outlane. Get the balls into the pops is the name of the game.
KB1. If you can alternate hitting the ramps, you can do well in this mode in general, but it plays nice with mb as well.
DtD1. Spinner/Alpha Ramp/Left out hole shots are lit almost all of the time during this mode, concertrate your shots there and you'll do well. Also, same shots are lit during the Galactic mode, so it's a good idea to try and start it.
Nero1. The mode itself is fine for mb, but the Galactic mode is great for mb, which is shoot those Red Matter targets. If i start the Nero Galactic mode by accident without a mb, I generally won't even try and hit the Red Matter targets, and instead just get back to trying to hit the Warp Ramp, and pick up a few Red Matter hits along the way.
I generally avoid SJ1 for mb's. Reason being because of it's Galactic Mode. The Galactic mode is hit the ship once and it's done.
Some Black Hole things:
You usually get add time during level 1 modes.
You usually get either 200k or +X muliplier when a mode isn't running.
Your more likely to get 'Light EB' during a level 2/3 mode.
You always get add-a-ball first when your in a mb.
So, to better your stack of running a regular mode with a mb, it's smart to try and hit the Black Hole to get 'Add Time' before starting the mb.