@vickster -- I experienced the same thing early on as my bookmark list grew. Because Bookmarks only display alphabetically, I began using a letter system to organize them. As it's currently not possible to edit bookmark names, I hesitate to suggest changing your existing bookmarks (unless they only have a few items each), but something similar might help as you go forward.
My system for recipes is that bookmarks begin with c. for recipes in a specific cookbook that interest me (e-version of sticky notes); i. for recipes using a particular ingredient; r. for different versions of a given dish (slaw, bundt cakes, etc.); z. for grouping recipes in relation to my cooking with them (z.made being the longest, others being z.on deck, z.club picnic 2014, etc.), and m. for grouping recipes in menus (seasonal, ethnic themes, etc.). The i. (ingredient-based) bookmarks are by far my biggest group.
The ability to edit names of Bookmarks would be a most welcome feature. For now, the only way to do that is to create a new Bookmark, add each of the recipes from the original Bookmark (one at a time), then delete the original.