Whereas I've heard of the episode order of the 1st Season DVD, I've heard nothing of the episode order of the 2nd Season DVD. I'd imagine it would go like this:
DISC 1 Pup Daddy/Candy Cane-ine Freaky Spy Day/Dog Tired Dog House/Time Waits for No Mutt Love Bird/Bluff Puppy Bark to the Future/Lights, Camera, Quacktion Close Encounters of the Doomed Kind/Golden Retriever Rat Trap/Agent of the Year T.U.F.F. Choices/Sob Story Hush Puppy/Quacky Birthday
DISC 2 Happy Howl-O-Ween 'Til Doom Do Us Part Barking Tall/Bad Eggs Bark to Nature/Mutts and Bolts Carbon Copies/T.U.F.F. Cookies Subliminal Criminal/Acting T.U.F.F. T.U.F.F Sell/Tattle Tale A Tale of Two Kitties/Pup in the Air True Spies/Bagel and the Beast
DISC 3 Mud with Power/Legal Beagle The Spelling Bee/House Broken Dancin' Machine/The Good, The Bad and The Quacky Pup Goes the Weasel/Puppy Pause Sheep Dog/Mom's Away Crime Takes a Holiday/Flower Power Match Me If You Can/Organized Crime Girlfriend or Foe?/Scared Wit-Less
That's just a speculation.