I do the same thing, so my answer would be no. They are two different decks that do not get shuffled together. If either deck is expired when you have to draw a card from them you lose. Sorry, I can't come up with a reason that they can not be in separate deck sleeves.
divedeeper said:
As an extension:
Would having your objective and command decks in different styles of sleeves considered marking in the unsportsmanlike sense? Specifically, I have my objective cards in art sleeves and my command cards in clear. This is my first attempt at competitve play and don't want to have the surprise expense on tourney day.
They are two separate decks that don't get shuffled together so no that is not marking. Marking is having cards in the same deck with different sleeves or some other manner of knowing without looking what the card (s) are.
The question was can he use different sleeves for different factions. NO that is marking your cards.
cmage said:
The question was can he use different sleeves for different factions. NO that is marking your cards.
cmage wins!
FINISH HIM!
So what you're saying is I can't put my Sith cards in clear sleeves and my Spies and Bounty Hunters in tinfoil? Just want to make sure…. 
Thanks Toq and R4.
In AGoT, can a Baratheon player sleeve each of his plot cards with a different color, as a reference to Renly's Rainbow Guard? I can't see why this would be a problem in Joust format, except that it could assist a player's attempt to deliberately lose to a friend, which is collusion, but I'd say it's easy enough to lose that game without breaking the rules to do it, so…
MarthWMaster said:
In AGoT, can a Baratheon player sleeve each of his plot cards with a different color, as a reference to Renly's Rainbow Guard? I can't see why this would be a problem in Joust format, except that it could assist a player's attempt to deliberately lose to a friend, which is collusion, but I'd say it's easy enough to lose that game without breaking the rules to do it, so…
No, it be marking his cards. To no apparent advantage, but still marking.
It would be a bad idea anyway; if the game went past 7 plots, then a smart opponent would look at all the plots before they go back in the unused pile and remember what was sleeved in what color so they knew what you planned to play.