Issues with replacing a clip in premiere with After Effects composition

So basically, i want to track a title to a piece of footage, so i've made my ins and outs and my footage is placed on my timeline in premiere with my title over top. Now I select the two pieces in premiere (the title and the clip) and I hit replace with after effects composition, and it ADOBE does it's thing etc.
but now in my AE project window I have two copies of my title file and two copies of my mp4 clip.
two of them are pre loaded into my timeline and the appropriate ins/outs which is perfect but I can't seem to do anything like tracking to them,
in my project window AE is referring to the ones that show up in the timeline as "compositions" while the extra files that aren't in the timeline are "mp4" and "psd" (the actual file types)
now. if i just delete the two "compositions" that are masquerading as files in my timeline and drag down my mp4 / psd then my tracking becomes available and all is wonderful
EXCEPT
my in's and out's from premiere aren't there and I have to go about all of that all over again and it's very annoying
any ideas?

Mat,
I'm sure you've figured it out. 
I don't know how you got two separate source clips - you should have a sequence (comp) and the footage in the project window (bin window) for each  In your comp, the tracking can be done by selecting the layer in that comp.
And - you've probably already figured it out that you needed those comps so they could dynamically link back to PremierePro easily.
If you have any Ae/Pr questions - I'm going to try to be in this forum more.  I love this stuff.
Ko

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