edit: ok, I found the version you have. It might be an older version? Not sure, it doesn't have a version number. I though the color cycling values were taken from the resource itself, but it looks like you have to enter them manually?
Yeah, you enter them manually. I had to guess until I found the correct values. Though, if you know the exact value of the beginning of each row of colours it would be easier, plus you can see easily which sequence of colour gradients are meant to be cycled. That would suggest to me that that information is not embedded in the palette file but manually set in the scripts somehow?
EDIT: Just searching through SQ5's resources, I noticed that there are a couple of all white palettes (except for the 0 and 255 entries which are black). Perhaps the fade to black/white transitions are done by gradually fading the colour values of one palette to their counterpart values in another palette. Then there are scenes like Bea in the cryochamber (Pic #47) where only she transitions to a shade of blue or red inside the chamber depending on what setting you set for that puzzle. The equivalent palettes (471 and 472) have all the exact colours except for the section inside the chamber which changes (colours 64-151). There were some really clever artists at Sierra who utilized colour cycling and palette transitioning very effectively. You can do some neat tricks with it.
Incidentally, the naming conventions of these palettes are clearly not an accident. Palette 47 corresponds to Pic 47 perfectly (the crychamber pic), but the red and blue variants are palettes 471 and 472 (as in 47 A and 47 B, distinct from the regular 47, to make it easier to use when scripting), which don't correspond to a Pic 471 or 472, which don't exist (probably intentionally, which suggests that maybe other Sierra games numbered their resources in a similar manner). This might shed some light on why there are so many different palettes. They're used for transitioning.
Though, most picture editors nowadays don't come with functions for working with 8-bit palettes. The only one I can think of is Deluxe Paint for DOS which catered to it rather well, and which Sierra artists used themselves (according to Mark Crowe in the SQ Commentary 2GFA Podcasts). I still am not sure how they concentrated certain colour values to specific portions of the palette (for instance the colour values inside the cryochamber). Maybe Deluxe Paint has further functions I haven't discovered to that end...
