I have had the Playstation 3 version of this game since release day and have had a bust with it so I decided to get the 3ds version of the game as everyone was saying it was a different game in which I'm enjoying it as there is one thing that I noticed that when I had my Double Trouble character in the 3ds game I had gotten him to level 2 then when I went to play the PS3 version I put him into the game and he was at level 1 so is that normal or should I be worried?.
In order for the progress from the 3DS game to be saved on the figurine, you'll have to drop Double Trouble on the 3DS portal and talk to Wendel again.
When you do, two things will happen:
 It'll pull Double Trouble into your 3DS game.  It compares the data on the figurine to the data on your save file for Double Trouble. Whichever is higher gets saved to both the figurine and the save file. In your case, that means that the figurine will get to level 2.
...I could probably explain that better. --- Stupid men are often capable of things the clever would not dare to contemplate. ~Terry Pratchett
So let's say that in the game my Stealth Elf is at level 4 while at the time she is only at level 3 in my ps3 version so if I go to level her up to 5 then when I put her into the 3ds then she will be at level 5?.
[a] You play with Stealth Elf on your 3DS game until she reaches Level 4. [b] You then drop the figure into the PS3 game without syncing first and she is still at Level 3. [c] You then play the PS3 game and level Stealth Elf up to Level 5. [d] You take Stealth Elf off the PS3 portal and have Wendel summon her back into the 3DS game. [e] The 3DS game analyzes data on the figure (Level 5) against the data it has on file (Level 4), and realizes that the level on the figure is higher. [f] A Level 5 Stealth Elf is summoned into your game, and saved on the game card. --- Stupid men are often capable of things the clever would not dare to contemplate. ~Terry Pratchett