1. Somebody enters tractor beam space, they got moved into a new space, do they follow the terrain rule of that new space?
Yes. Always apply terrain affect of a space you end a move in.
2. Using equipment once it's ready doesn't cost any charges correct? So what's the use bonus action really good for then?
The Use bonus action appears on the Tractor Beam and Defense Gun spaces. A player there gets to use the Tractor Beam or Defense Gun on any player, the Guard (or themselves) as their Bonus action. See the discussion on the Terrain Summary table (rule book pg 13 and back of status cards.)
3. Can you add multiple energy shields to one card?
Absolutely! Add a shield to any face down card in your hand.
(One game at Gen Con, a 10-yr old put four Energy Shields over one card. Two Grenade Launchers and a Zappp later, he was laughing and laughing to reveal a Nothing card--his Alien safe elsewhere!)
4. The rules stated that terrain rule takes effect during the start of your turn, but can they zip into a crater and use that terrain to hide from everybody?
Yes. The terrain effect of any space you end a move in applies immediately. A Zippp into a Crater space after blasting everyone in sight is a classic (albeit cowardly) tactic and highly recommended! Note: if you take Zippp action through a space and end on another, no effect from the space you moved through.
5. Force fence is not detailed in the advanced terrain rule. Do they still cost you -1 charge? Can you still pass through even if you don't have any spare charge?
The Basic rules apply and carry forward (see Terrain Table pg 8 and back of status cards). Since Escape phase occurs immediately after being awarded more charges in the MoonQuake phase, a player will always have a charge to lose to the Force Fence in this phase. All the more reason to ready a Hazard Suit on the way to the top. And remember, a Tractor Beam on the Launch Pad moves the player into the Force Fence (unless they have Grav Boots to ignore Tractor Beam or Hazard Suit to ignore Force Fence).
Great questions. Please don't hesitate with more!