How many of each half of the Pokemon LEGEND cards can I have in my 60 card deck? Is it 4 total or 4 of each half?
You can put up to 4 total halves of each Pokemon LEGEND in your deck (e.g. 4 Ho-Oh LEGEND halves and 4 Lugia LEGEND halves), but you cannot put 4 of each half of a Pokemon LEGEND in your deck (e.g. you couldn't have 4 Lugia LEGEND top half and 4 Lugia LEGEND bottom half). (GS:Heart Gold/Soul Silver FAQ; Feb 11, 2010 PUI Rules Team)
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I put three halves of one Pokemon LEGEND card and one of the other half in my deck?
Yes, that is legal if you wish. You do not need to have the same number of each half in your deck.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I put 4 each of the Unown with the "RETURN" Poke-POWER and the Unown with the "FLASH" Poke-POWER in a 60 card deck?
No, you can't. In the case of cards like "Unown G" and "Unown R" where the Unown's letter is in its name, they are considered different names, and you can have 4 of each in your deck. When only "Unown" is written these are cards with the same name, so you can only put up to 4 copies of any with that exact name in a 60 card deck.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Do Pokemon LEGEND count as one Pokemon or two for purposes of bench space, prizes taken, attack effects, Poke-POWERs, Poke-BODYs, and calculating damage?
A Pokemon LEGEND is made up of two Pokemon cards each consisting of 1 half of the Pokemon, but it counts as a single Pokemon while in play; one bench space, one prize per KO [unless noted otherwise on the card] , etc.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Is LEGEND part of the Pokemon name? Can I have 4 Lugia and 2 Lugia LEGEND sets in a 60 card deck?
LEGEND is part of the name, similar to past sets that contained Pokemon with "Dark" or "-ex" as part of their name. They are not considered the same as their normal counterpart, so yes you can have 4 "Lugia" and 4 "Lugia LEGEND" halves in your deck.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I use cards that search for a Pokemon, like "Bebe's Search" or "Poke Ball" to get a Pokemon LEGEND card from my deck?
Any effect that lets you search your deck or discard pile or do something from your hand with "a Pokemon" will let you use that effect on one half of a Pokemon LEGEND set, but not both halves.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I use "Pokemon Collector" to choose Pokemon LEGEND cards as part of the 3 Basic Pokemon I search for in my deck?
No, because Pokemon Collector only lets you choose Basic Pokemon. Pokemon LEGEND are considered "Unevolved Pokemon" when in play, but they are not considered "Basic Pokemon".
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
How many Shellos/Gastrodons of the East Sea or West Sea variety can you have in a deck?
You may have four of each. "Shellos East Sea" and "Shellos West Sea" are different Pokemon.
Source: PUI Rules Team (2009-04-30)
I like to keep my deck and discard pile sideways to help me keep them separate from my bench. Is that OK?
Your deck must be oriented vertically, to avoid revealing information during handling or cuts. You may turn your discard pile 'sideways', to help you distinguish it from your bench.
Source: PUI Rules Team (2008-10-16)
Can I separate my discard pile in two stacks to make it easier to count energy?
No, you have to have a single neatly stacked discard pile. You may sort or turn cards neatly in that pile if it helps the game go more quickly, but they must all be touching.
Source: PUI Rules Team (2008-10-16)