If I have a Mystery Energy attached to an active Trevenant with a Retreat Cost of {3} could I pay for my one Retreat Cost using the Mystery Energy?
Yes, Mystery Energy will reduce the Retreat Cost, and you can discard it to pay for the final energy. The Pokemon is on the Bench before the Energy Cost returns to normal.
I am playing a Robo Substitute from my hand to my Bench, but my opponent used Venomoth's "Dizzying Wind" attack last turn. Do I have to flip to play it?
Yes, Robo Substitute is a Trainer card when it is played.
Source:
Phantom Forces FAQ (2014-11-13), TPCi Rules Team (2014-11-13)
If I use Kyogre EX's "Smash Turn" or Celebi EX's "Wind Whisk" or Gengar EX's "Dark Corridor" attack, can I switch it with my benched Sigilyph that has the "Safeguard" Ability?
Since the attacking Pokemon is the target of the switch effect, Sigilyph can be moved in this situation.
Source:
TPCi Rules Team (2013-01-31), TPCi Rules Team (2014-11-13)
Checking for Confusion should be the very first thing you deal with after you announce what attack you want to use. Contrary to the "Full Details of Attacking" steps found in some older rulebooks, it must be done prior to making any choices the attack requires (such as choosing an opponent's Pokemon), paying any costs (such as discarding energy), flipping a coin to see if the attack fails, etc. So as soon as you announce which attack you are going to use, you must check for Confusion immediately before proceeding with any requirements of the attack or effects on the attacking Pokemon.
What's the proper way to play a Trainer like Ultra Ball?
When playing a Trainer you first put it onto the playing field (not directly into the Discard Pile). Then you do what the card says, such as discarding two cards (those go into the Discard Pile right away), searching your Deck, showing the selected Pokemon to your opponent before putting it directly into your hand, shuffling your Deck, etc. Finally, after everything is done, put the Trainer card into the Discard Pile.