I’ve had to do this a few times over the years, but I usually do it after the track IDs are in place. I just split off a part of a song that needs a special EQ and do a quick crossfade with the surrounding parts. Then, I can add the extra EQ needed to at the clip level of the part of song I’m trying to automate.
If you do this work before adding tracking IDs, you will get extra track IDs at these edits, depending on your CD Wizard settings.
For me it’s never been a problem to delete the extra markers that are unwanted due to 1 song being cut into a few clips. I’ve never experienced the clips recombining after deleting a marker but I can test later and what happens.
If anything, add your track markers first and then do your edits for manual automation.
The thing that’s hard is when you need to gradually return a song to “normal” state. The way Pro Tools handles plugin automation is great. In Pro Tools, I can put a special lo-fi EQ on a song and have each EQ band gradually return to normal on it’s own terms. With the manual automation in Wavelab, it’s usually all or nothing for your special lo-fi EQ bands, or other plugin that you are trying to automate in for a portion of the song.
It can also create other headaches in the future when you start chopping up your song just to automate some EQ or other FX.