It's been covered adequately in this thread, but I'll reiterate to the OP: you're doing it wrong.
1. All my bottles are recycled commercial non-returnable 9" longnecks. Yeah, it's some work soaking them in PBW to clean them and get the label off- the first time.
2. The most important piece of equipment for bottling is the vinator (shown previously). Get one. No, just GET ONE.
3. Sanitize bottles with Star San using vinator (I place upside down in dishwasher, but feel free to use a bottling tree, also shown previously).
4. Bottle. Some people, like me, would also run the dishwasher before bottling, others regard this as redundant. Suit yourself.
5. After pouring your beer, immediately rinse bottle thoroughly and store until next time.
6. Repeat steps 3-5 indefinitely. Takes all the fuss out of bottling.*
*Note: I don't care what anyone else says or does, I've used this process on the same 400 bottles over a half-dozen times, and I have had no (that's ZERO) infections or other issues. And I'm very content with my bottling, don't need any kegs, thank you very much.