Yes, I haven't tried the Snowflake thing, but I looked at it and it was very interesting - it reflects quite closely the way I think about plot.
When I'm setting out the formal plan - which is quite skeletal by some people's standards, and positively lavish by others' (see
here, anyone who's interested and hasn't yet encountered my blog post about the plotting grid) - I do sometimes get more detailed ideas about how a scene might go. If I want to remember them, I make separate notes about whatever occurs to me. That way I don't worry I might forget them, but the skeleton stays skeletal.
No doubt something like Scrivener would help, but I'm a backs-of-old-MS-and-biro creature at heart...