There are several ways to transcribe with media linkage. In chapter 5 of the manual, we describe five methods:
1. Sonic Mode (section 5.1)
2. Transcriber Mode (section 5.2)
3. Sparse annotation (section 5.2.3)4
4. Walker Controller (section 5.4)
5. Exporting to a Partitur editor (section 5.5)
6. Manual editing (section 5.8)
For basic alignment and transcription, we mostly only use #2 and #4. We probably should distinguish two flavors of methods #2. If you stay within method #2, you can proceed as you have by transcribing and then you can go back and add the time marks just using F5 for each main line.
I wouldn't recommend mixing methods #2 and #4, although it may work. In your case, why don't you just decide which method to use from the start. If you want to continue with method #2, then you go back to the fix utterance and use transcriber mode with F5 to insert bullets for each line after it finishes by hitting the space bar.
I may get around to rearranging the material in Chapter 5 to make this clearer, but all the information is there.
Alternatively, we might be able to help you more directly with what you are doing, but I think we might need screen sharing for that.
Best,
-- Brian MacWhinney, Teresa Heinz Professor of Cognitive Psychology, CMU