Generally, and this is true for all purifying/sterilization means that operate in the container like this (chemical treatements, for example), you use some of the treated water to flush the threads and exterior of the container. It isn't perfect, but the dilution principle, reducing the bugs to a minimum that your body can usually deal with, seems to suffice as it has a long track record of working.

I've used the first generation model for years. Still going strong with nary a sick day. Filtering is important.

Like bsmith I use a separate cup to fill the bottle, then I swirl the bottle during use to insure that everything in the bottle gets a dose (all the water above the waterline. Like Doug, I then use a small amount of the clean water to flush the areas where contaminated water might have gotten on it.

I like the SteriPen very much when I am in an area with lots of water. I use it canoeing all the time. Use a prefilter in dirty water. In dry areas it takes a while to make lots of water so I use a filter. In areas where the threat levels are high (outside the US) I use a dual method. Filter and chem, filter and pen, etc.

I also like it when traveling in places where the water is suspect. I use my own bottle for washing my teeth and make drinking water in my hotel room. It is much easier than the filter I used for years for this purpose.

Respectfully,

Jerry