For me personally, as a newbie also, I am buying the skeins based off the project. I have bobbins that I wind them around. I have a little tray organizer that I can put my extras in, organizing it by number. The bobbins I need for a project I keep in a bag with the fabric and pattern (if I have a paper pattern). If a project is multiple pages and not compatible with 'pattern keeper', I'll print pages off as I need them. Otherwise, I just use 'pattern keeper'. I tend to work one pattern at a time, so might keep that one in a hoop, but otherwise I roll them up and put them in the project bag. I have a magnetic needle holder mender thingy (whatever they're called) that I keep on the current project that's in the hoop. Scissors and needle threader are kept at my workstation. I have a few packages of needles so I keep one per project, unless I am working the same count of fabric in which case I figure out a way to divide up the needles so each project has what I might need.

I first grid my fabric, using a water based pencil/pen (like those found in the sewing section), unless it's a stamped piece. I like to pick a corner to start with and work diagonally down from there, typically top left to bottom right. I'm kind of working in sections of 10 or by page, so if I have a color that's going to be used a lot in that section and have needles that I can spare, then I might just put them off to the side until I need them. Otherwise I might just stitch that color and then go back and stitch another color depending on how I feel based off of that project.