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One way is to apply the timecode effect to your timeline clips, set it to media, and read off the source timecode in the program monitor as you move along the timeline.
When you're done, remove or disable the effect for all the clips.
If you have finished the timeline editing, then a variation would be to nest the original sequence in a new one, apply timecode to the nested clip, and do it that way. Easier to remove the timecode effect, but your overlay images will shift if you re-edit the nested sequence.
Since you don't say which version of PPro you have, it is possible that you don't have the timecode effect. If so, then you can use DVdate from http://www.dvdate.ru/en/dvrecdate.html instead.
I wrote the suggestion below, even though it seemed like it should be obvious, then went back and reread your question. I can't tell if you are a) asking for what I answer below, b) asking how to reference the edited timeline (which would be the timeline code), or c) how to add markers to an original clip opened in the project panel and have them appear in the timeline (you can't - but see below). So, I hope this helps....
Double click a clip on the timeline. Look at the time code in the source window. Is that not the timecode you're looking for?
Mark it there, and it will be available in the timeline. Once you split the original clip (and other subclips), the changes in the source window are only made to the clip instance you have opened in the source monitor. For your purpose, that should work fine. If you open a clip from the source monitor, it will have only the markers you placed when opened from the bin, not any you added when you opened clips from the timeline.
And yes, the style of the forums means that we should all indicate our version of Premiere when asking a question, even if we think it may not matter
I apologize for not stating the version I'm using. I'm using CS2 (3.2.0). It looks like both of your methods will be useful! Thanks!