I'm in the same situation as you are -- it's been nine months since my bunch moved in while they're building their new house. My sewing machine and one cabinet is in the dining room. My stash is in a closet and in plastic tubs under the bed. My sewing notions are in another closet. I use the dining room table for cutting, and pull the ironing board out of the laundry room when I need it.
The biggest thing I've had to deal with (other than a two year old wanting to "help") is having to get everything out and put it all up when I'm done. It bothered me at first, but I kept telling myself that it's temporary and well worth the inconvenience to be able to provide a home for our kids while they need it.
It did take me a while to get things organized in their new locations. I spent a lot of time trying to remember where I put something. If I had it to do again, I'd make a master list of where everything is (then I'd probably lose the list!). It did help me to keep as many notions--pins, scissors, rulers, rotary cutter--close to the sewing machine as I could. I have too much thread to keep it all in the dining room, and it's a pain to have to get it out of the bedroom closet when I need it.
With some trial and error, you'll get a system in place that works for you. Good luck!