You can keep notes, as they occur to you. Always bear in mind that the story needs to progress, so if a good idea for the plot occurs to you, make a note. It is another strand.
Don't be afraid to have lots of strands. But they must all be essential to the action. Make them work. Make sure they weave together amd leave out the ones that are too tangled to be helpful. Just get the scissors and chop it. Hack it about a bit and keep any interesting messes to look at another time for another story.