I will preface this by saying I really only plan the base scene structure in each chapter before writing, so a lot of it is free flown as I go. But when I do think a choice should have affects later on, I usually add the variable into the game right then and there, and if need be I have a notes section on the startup page made entirely of *comment commands so I can remind myself what they were for. Worst case scenario, you don’t use the variable and just delete it during the editing process!
I also split my variables up into different sections in the startup page. So I have regular gender and name commands under one section, then hit enter twice and title the next section for myself with a *comment commands and set up that section. So it looks like:
*comment Player Choices
*comment this thing happens
*comment This should effect this thing
It ends up helping me a lot to separate things into different sections under the startup page. These have been ramblings of how a person that barely plans a story keeps organized and up to date with choices they’ve created and how they remember what they do.