First off, your "If either Reshiram or Zekrom do one of those moves on each other, there signature moves get more powerful." is wrong.
Look at this:
Pokemon DB
Power increases if Fusion Flare is used in the same turn
http://pokemondb.net/move/fusion-bolt
Power increases if Fusion Bolt is used in the same turn.
http://pokemondb.net/move/fusion-flare
Smogon
This move deals damage. If this move is used after another Pokemon has used the move Fusion Bolt in the same turn, its Base Power will double. If another Pokemon uses the move Fusion Bolt after this move has been used in the same turn, then the Base Power of that Fusion Bolt will double. If the user is frozen, using this move will thaw it out immediately.
http://www.smogon.com/bw/moves/fusion_flare
>This move deals damage. If this move is used after another Pokemon has used the move Fusion Flare in the same turn, its Base Power will double. If another Pokemon uses the move Fusion Flare after this move has been used in the same turn, then the Base Power of that Fusion Flare will double. Although a physical move, this move does not make contact with the opponent.
http://www.smogon.com/bw/moves/fusion_bolt
Lets say zekrom used fusion bolt on reshiram, then reshiram used fusion flare. Fusion flare would be doubled in power, but not fusion bolt.
Now, to answer your Question, only if Fusion Flare was used before Fusion bolt then Fusion Bolt would get double Base Power, And vice versa. Other moves used by Reshiram / Zekrom would not power up Fusion Flare/Bolt. To be straightforward, No.