CHM files are designed to be installed locally on each users PC, something that more than likely explains your related question, typically as part of an application. As they are installed locally, it means updating is more difficult. Web based output (e.g. WebHelp) is stored on an intranet, server or web location and can therefore be more easily updated. It sounds like you may be better to go the WebHelp route but without knowing more detail that decision is best left in your court.
As for "bookmarks", do you mean the ability for a user to store a page of the help that they can refer to again at a later date? If so, this can be achieved inside a CHM file. In the window properties inside your project, there is a "Tri-pane Tabs and Windows" section. In there is a Favorites option which when ticked adds a tab to the left hand tri-pane of the CHM. Adding a bookmark in this fashion is a little more complicated than in a browser, but it does work. It also has drawbacks in that the data behind these favourites is stored in a HH.DAT file. If this is deleted, the user looses their favourites as well as other information.
Finally as I intimated earlier, CHM files are best run on a local drive. The reason for this is that Microsost issued a security update a few years ago rendering them next to useless unless they are. You can find further detail about this update here.
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