You need to set the internal Parts Receive Channel to off. In Pattern Mode, push Mix and then Edit to enter Pattern MIX Edit Mode.

When you first enter you may be in Common Mode which has the parameters that are Common to the whole pattern (Effects, Arpeggio, etc.), Push one of the [1]-[16] number buttons to select the Part you want to play only on the external synth.

Press [F1], then [SF2] to go to Part Voice Play Mode, here you can set the mono/poly, Part Arp Switch and MIDI Receive channel. Set the receive to Off (it's after channel 16 in the list). Voila, the internal sound does not receive MIDI.

Motif is deep, there was a post on an EX 5 site where the people were saying that couldn't do detailed editing on the Motif. Actually they had played with Motif and never entered Edit mode because of all the things you can do without entering Edit.