However, your question is probably more along the lines of "Why do you have two sites?" and/or "Which site will help me find the information I'm looking for fastest?"
Why two sites?
The Page of Honest Intellectual Inquiry was the first site (and was hosted on a different domain until late in 2000). It began as an exploration of various ideas but was primarily centered around Mormonism as that was what I was chiefly investigating in 1995 and 1996. It soon evolved to include information on Christianity. Eventually, the vast majority of the new material dealt with science-related items.
2think.org was created in 1998 for several reasons. First, it allows for an easy to remember URL. I'm also able to use scripts on the pages which makes the site a bit more 'nifty' (with random images and other frills) and enables me to make global changes to all the pages much more easily. It also served as a backup should the other site be temporarily down. The focus has also shifted a bit from the previous site. Methodology (and similar topics) are the focus.
Which site is for me?
The quick and dirty answer is "hopefully both". They are organized a bit differently. If you are looking for a book review and you want to browse by subject then 2think.org is the place to go. If you want information on religions--especially the Mormon faith--then the old site is where you want to browse. The search engine on 2think.org (run via the above mentioned scripting capabilities) is much more comprehensive so you may want to start there. If you are looking for a religious item related to the LDS Church then start here.