One option is to fill the remainder of the jar with your own urine - this identifies the bottle as belonging to you. However, if the idea makes you a bit squeamish, there are other ways you can complete the process. Instead of urine, use a bit of wine. You may wish to consecrate the wine first before using it in this manner. In some magical traditions, the practitioner might choose to spit in the wine after it's in the jar because -- much like the urine -- this is a way of marking the jar as your territory.
Cap the jar, and make sure it's sealed tightly (particularly if you used urine - you don't want any accidental spillage), and seal it with wax from the black candle. Black is considered handy for banishing negativity. If you're having trouble finding black candles, you may want to use white instead, and imagine a white ring of protection surrounding your witch bottle. Also, in candle magic, white is typically considered a universal substitute for any other color candle.
Now - where to stash your bottle? There are two schools of thought on this, and you can decide which one works best for you. One group swears that the bottle needs to be hidden somewhere in the home - under a doorstep, up in a chimney, behind a cabinet, whatever -- because that way, any negative magic aimed at the house will always go straight to the witch bottle, avoiding the people in the home. The other philosophy is that the bottle needs to be buried as far away from the house as possible, so that any negative magic sent towards you will never reach your home in the first place. Whichever one you choose, be sure that you're leaving your bottle in a place where it will remain undisturbed permanently.
If you do believe someone may be trying to harm you or your family with malicious magic, be sure to read about Magical Self Defense.