I routinely use FBReader on a Windows PC, a Nokia 770 and a Pepper Pad 3. On all three I mostly use the stylus (or the mouse on the PC) for navigating menus etcetera. On my new iLiad, I find the stylus much less useful. The only indication I have seen previously on this issue is that the small "+" marks used to expand the library lists are hard to use. In fact, many stylus operations seem very hard or impossible in FBReader on the iLiad. For example, when selecting a file in a a large directory there is a navigation bar to the right which I would normally use to jump to about the right place in the directory. A tap on the bar does seem to be detected (e.g. refreshes the box) but has no other noticable effect. Similarly in the tools dialog, the arrows to bring up other tabs don't function for me. Is what I am describing the common experience? I may be too used to navigation on the N700 and PP3, and hence using the stylus sub-optimally.
In any case, fortunately there are almost always key press alternatives to the stylus. The previous and next (arrow) keys are <up-arrow> and <down-arrow> and the confirm (dot) key is <return>. These are very useful for navigating menus. The flipbar is <page-up> and <page-down>, and these are useful for navigating directory lists (e.g. when manually selecting a new e-book). To navigate between tabs in the tools window (e.g. to bring up the keys tab on the far right of the window) I used the <left-arrow> and/or <right-arrow> keys, which are only on the on-screen keyboard. When selecting a font size, entering the new size via the keyboard was much easier than using the very small up and down arrow icons. I really like the on-screen keyboard by the way. It is easier to use than the one on the Nokia 770. I am used to the keyboard coming up automatically as needed, but having an icon to control the keyboard is actually a better approach.