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Nest those clips into a new sequence (you can select them, right-click/Cmd-click, select Nest) and then apply the effects to the nested sequence. Think of it as Collapsing in Avid...
What if I want to apply an effect to just a portion of two clips to create a transition and then copy and paste that effect/transition to use on multiple edit points without having to keyframe the effect each time? For example, in AVID if I want to create a nice white flash that is more organic than the traditional cross dissolve to a white frame and back, I would apply a glow effect to a separate video layer that spans the edit point. For an 8 frame transition I would begin the effect 4 frames before the edit, then key frame the glow intensity from 0-100% over 4 frames and back to 0% 4 frames later.
I have worked mostly in AVID in the passed, but am trying to get a better handle on Premiere Pro because of its comprehensive integration with After Effects. I appreciate all of the help.
Well, depending on what you want to do, you might actually be able to use a clip instance of one sort or another.
One option is Transparent Video (File > New > Transparent Video); by itself, Trans. Video doesn't do anything, but some effects can be applied to it and will generate an output. This doesn't work with all effects, so you'll have to experiment. Check here for more: Create a transparent video clip
Another option would be to use a Color Matte (File > New > Color Matte) or Black Video (File > New > Black Video) clip. These do have an effect by themselves, so you could apply any effect you wanted to them, and then possibly use a Blending Mode to apply it. Black Video is common for this purpose, with something like the Add mode. Again, not perfect, but it will depend on the effect you're trying to achieve.
Unfortunately, we don't have anything like AE's adjustment layers in Premiere Pro. That would solve your problem, quickly.