How could I pull out a little from my carboy to take gravity readings during fermentation?
I tried to use a auto-siphon but it was a mess.
You can use a wine or beer thief and a test jar to grab a sample from your carboy.
I use the following one and it works great: http://www.amazon.com/Fermtech-Wine-Beer-Thief/dp/B00186ADYS This one is nice because the hydrometer fits right inside it so you don't need a test jar.
I never put the sample back in, just scared of contamination. Does anybody put it back in or just drink or dump it? Usually its a good time for me to take a taste.
Another option is to one end of a sanitized food-grade plastic tube into your carboy and siphon out a bit into your testing tube for the hydrometer. This will work for the narrowest of carboy necks. However, there is some risk of contamination (especially if you suck the end of the tube and that then falls back into the carboy) . A wine-thief or turkey baster are probably safer bets if you can use them.
Another idea: if your wort is deep enough, your carboy has enough head space and you have big, readable letters on your hydrometer, why not just drop the (sanitized) hydrometer into the carboy and leave it there!