Ok I think I get it.
You start with the logo over a background. Then the logo transitions off leaving the background with another image in "hole" that the logo was in. If that is it try this.
On V1 put your background footage.
On V2 put your logo
On V3 put the footage you want in the "hole"
On V4 put the logo again.
Set the composite mode of the footage on V3 to be "travel matte alpha"
Then set your transitions on the logo on V4.
How does that work for you?
-Vance