>>>Once I understand it, I'll probably use comments.<<<
Yikes, well then keep your original Theme and all the changes you make around with the comments in them.
I just checked your site from the link up top, and you have other problems going on, like the inability to even click a title on your page to get to the individual post, but let's stick with comments for the moment.
In the lastest version (check DOWNLOADS at the top of the screen), without any plugins I got maybe 5-10 comment spams a week. I have a top page ranking site with over 700 articles. Before the latest version, it was a magnet for all freaks, whackos, and time wasters. Now, almost nothing. Comment spam, for the most part, is controlled and controllable.
With no comment spam coming in, I started to get worried. What if the new process was cutting out GOOD comments? So I installed Paged Comment Editing Plugin from Coldforged which allows me to SEE what WordPress is catching. I was stunned at how little was actually coming through. Using the plugin, click on "include spam" and you will see what is being caught highlighted in a pink background. I can easily delete these, removing them from my database and saving some space. Nice.
Then one day I got hit by about 25 viagra/casino spams. After several months with only the occassional irritant, I was pissed, so I added Bad Behavior Comment Spam Plugin. Again things trickled down to a nothing and I got paranoid again. Comments were being bounced by Bad Behavior before they even got to the comment stage, but it was "too quiet". So I added Bad Behavior Stats to My Dashboard so I could keep track of what it was doing. WOW, it was catching A LOT. On average, it nails 400 known comment spam spiders, robots, etc., weekly.
But you see what happened? WordPress stopped the majority of the comment spam out of the package. I got paranoid when it wasn't there so I added plugins to help me deal with MY paranoia not with the lack of spam!
Quit ripping and tearing up your Themes and pick a great one and enjoy the ride. Comment spam is the least of your problems with WordPress. Coming up with good content that attracts visitors and keeps them returning is YOUR biggest problem. ;-)