Bookmarks get created automatically, every time you hit the Play/Pause button. Nearly every other event that happens will also create a bookmark (switch podcasts, switching parts, interruptions, etc.). These are called auto-generated bookmarks or auto-bookmarks. These auto-bookmarks are also easy to delete: just tap on the "Delete Old Bookmarks" menu item, which will delete older, non-customized bookmarks.
"What if there are some bookmarks I want to keep?"
Simple, just customize it in some way: change its color, title or notes.
"How do I delete a bookmark?"
Just swipe-to-the-left on the bookmark in the table it's shown in.
"Can I adjust the position of a bookmark?"
Yes. In the Bookmark details view, tap on the Postion: 01:23:45 label. An adjustment panel will appear. Tap on the hours/minutes/seconds/tenths to adjust and use the up/down arrows to change the position. Tap 'Save'.