Cleaning bottles is one of the most hated tasks in home brewing, but it doesn't have to be that hard if you following two simple steps:
Step 1. As soon as you finish a beer (and I mean immediately), wash out the bottle in the sink. Turn on the hot water, fill about one quarter with cold water (while the hot water is warming up), plug the end with you thumb and give the bottle a really good shake, empty, then repeat with hot water. Leave to dry and make sure to tip out any residual water the next day. Your bottles can be stored until needed.
Step 2. When you're ready to bottle, first hold the bottle up to a light and ensure it's clean inside. Use a long bottle brush to clean out any debris or yeast material left inside the bottle. If you followed step 1. correctly, there should be very little (if any). Then mix up a solution of sanitiser (I use Star San). Ensure every internal surface of the bottle is covered with sanitiser solution. When all your bottles are ready, throw your crown seals (bottle caps) in the solution to sanitise as well.
You're now good to go. Make sure to leave a small amount of head space (air) at the top of the neck (IE: don't fill to the very brim), and that you get a tight seal. This lets the CO2 released by the residual yeast generate pressure that carbonates the bottled beer. Note: you can use either standard or twist top bottles for home brewing, as long as you get a tight seal it does not make a difference in my experience.
You're done, go crack a cold one and enjoy!