Done this many times. First do not take bottles that are marked for fuel. Second clean them out really well. If they smell like fuel they will be gone. Once clean leave the cap off.
Now I personally mark my bottles boldly with the words "PEE BOTTLE". Then I pee in them leaving a little in the bottom.
Here are TSA words of wisdom:
http://www.tsa.gov/travelers/airtrav...rial_1187.shtm