quick prototyping in project design & development

Question

i'm currently working on a project in my spare time (mostly 3-4 hours from monday to friday, and up to 6 hours on sundays) and i've found redmine very useful to hold a record of development tasks.

However, there are some stuff, specially when you are trying to prototype or brainstorm a redesign of a set of related classes, that the best tool that i've found for this still is a sheet of paper and a pen.

I want to understand if maybe i'm just short of getting to work properly with existing tools. Do you find the use of a notebook or a journal an unavoidable part of software design? are there better alternatives? how do you organize pen-and-paper work and other software management tools like redmine?