I'm not sure which version of Logic you are using. I use Logic 9, so I'm not sure that the specifics of this will translate to 10, if that is what you are using, but I imagine this function exists somewhere within 10.
In the top right corner there are two mouse tool options. The left is the primary mouse action, while the right is to create an action for a command+mouse click. If you set the pencil tool to the secondary mouse action, then you should just be able to hold the command key and enter the notes. This secondary mouse function appears in the arrange window also, so you can create a separate function there. Sometimes I will use the automation curve tool in the arrange window.
I also like to copy and paste notes within the MIDI piano roll using the alt+drag and drop shortcut. That allows me to have a few notes and move a whole set of them to edit/change elsewhere in the MIDI field.
There are a lot of tools in the secondary mouse function that I have used. Specifically the Velocity tool has been helpful in my MIDI manipulation.
I also prefer to work in the popup window for the piano roll instead of the one that is embedded in the arrange window, as it gives me more space to work with. In Logic 9 you can access this either using the command+6 shortcut or alt+double click on the region you would like to open. If you select multiple MIDI regions in the arrange window, you can open all of them at once and the notes from the different regions will all appear in the same window.
Hopefully this helps. There are a whole lot of other tools and shortcuts that can be very useful for MIDI manipulation. I won't spend the time to write them up, as they don't specifically relate to your question, but I would recommend looking into the Transform functions.