Here's what I do (I use plastic PET bottles):
- When I finish drinking a bottle I rinse it, pour some water in, put the cap on and then shake it to make sure there's no funk in the bottom. I then get my StarSan spray bottle and give it a few bursts, grab the cap, spray that too, put the lid on, shake it some more and then store it.
- When it's bottling time I grab maybe two or three bottles at a time, shake them to redistribute the contained StarSan, take the caps off and throw the caps into a bucket of StarSan, shake out the excess StarSan into my kitchen sink, stack the bottles in my dishwasher and repeat until the brew is bottled.
Never had a problem and it's a relatively painless process - hope this helps!