I know that I can do this with the track matte key but that only works with titles and so this puts me in a black whole.
That's not true; you can use it with any image. Track Matte can use the alpha channel of the matte image or the luminance (white and black) of an image.
Do you still have the PSD? If so, just import it flattened/merged with a transparent background. Put it on a track above your video clip, and add Track Matte to the video clip. Set the Track Matte to Matte Alpha and specify it to use the PSD layer. Invert if necessary.
Your chosen Save_As format MUST support Transparency.
I would create the logo, in whichever program you are using. Then Import/Place in Photoshop to do the Rasterization, then Save_As PSD, which will be Imported into PrPro.
I have a problem and I don't know why. I'm using track matte to matte alpha on some videos and the thing is that the psd file that I use to see the videos through only has it's effect on a few of them but the options are the same on each video. If I use a copy of the psd file and I put it on top of the first psd file but I cut the first one so that it won't be on top the effect works. The images explain better. Why is this happening?