@Joe > Unfortunately the T1's effects only control Traktor, and the Traktor effects are added on top of the selected deck within Traktor. Therefore the DJM-T1 will not recognize the Traktor effects if you are using external decks outside of Traktor.
Unfortunately I think your only solution would be to use the Traktor decks as the effects will be layered directly on them. A Pioneer EFX unit would not work because there is no Send/Return on the DJM-T1.
The DJM-T1 was built to be used as a high quality mixer to work with Traktor controlled decks on CD or Vinyl. It can support external decks as it contains a built in 3 band/ISO mixer, but was meant to use the Traktor effects with Traktor decks only. This is not a limitation to the DJM-T1 hardware, it is a limitation of the Traktor software unfortunately.