My cover is from BRU and was relatively inexpensive, around $15. for a Graco cover that fits any carseat. Is this your model? It came with a black drawstring bag to store it in. It's a little unwieldy to fold, but I lay it out on a table and make everything as flat at possible, fold in sections, then store it in the bag. There's extra room in there so our ponchos fit in too. It all fits easily in the bottom of the P3 (even with our small cooler in there). We just grab the bag on our way out the room when the weather report is iffy.
Because that rain cover works SO WELL in a big downpour, I wouldn't want to use anything else ever again. I even took it on a trip to Niagra Falls last week---we went on the boat tour into the falls and I'm so glad I had it for the stroller...the baby just sat there, happy and wonderfully dry.