Okay: Short and Sweet:
You are going to open that box you have been staring at. Now as the smell of fresh plastic tickles your nostrils think about this. Where are you going to put All those parts? First do your trimming and stuff on the Sprues.Then your painting. Now. Take the little meal trays from Stauffers or the Ready Made meals at your fave foodstore, that you have cleaned out.
Now taking the parts off and throwing them into the bins isn't smart. What I do if I can(The U-2540-or the Wilhelm Bauer) A REVELL germany kit wouldn't let me. the numbers were scattered all over three sprues!
So I isolate the sprue areas now around parts. For instance, the number one Gun on the Missouri(Which I am currently painting) All those numbers are noted. Now after painting, I will if possible isolate those parts and cut that area of the sprue off, putting it in the tray, then on to the next one and so on. I keep a box(Cat not withstanding) and throw the empty sprue in it. The gun is painted and built and the sprue is empty and in the box, or on top of the Cat! This method, works in most cases, sadly to say, parts are more organised in Model RailRoad kits than ours.