How to sync subtitle timeline with video timeline?

Have you checked the settings in Subtitle Edit?

With it set to 23.976fps (which is progressive scan) then all your timecodes are going to be totally off when the resulting script is put to a 29.97fps file - you need to set Subtitle Edit to the same framerate as the file you are using.

If the title is brought into a 29.97fos DVD then you could well have a problem here as the title will end too early - and the sync issue will get worse & worse as you go further into the timeline simply because once a 24fps script is imported into a 29.97 fps clip then everything gets more & more off sync. As an example, timecode in 24fps might read as follows:

00:02:29:21

The same place in the project referenced to 29.97 timecode will read instead as

00:02:29:27

This is a difference of 6 frames (or a quarter of a minute) at just 3 minutes into the project. By the time we get to an hour into the project the difference becomes as follows:

24fps = 00:59:14:08

29.97fps = 00:59:10:24

Similarly, a timecode of 01:00:00:00 in 29.97fps becomes 01:00:03:14 in 24fps so 3 whole seconds out at the 1 hour point.

It is absolutely critical that all timecodes are the same throughout the project.