Hi ickreitz and welcome to the Papyrus Author Forum. Thanks for your questions.
Yes, you can edit the My Characters database to suit your requirements. Each table can be amended to add fields, remove others, change field attributes and also alter the layout of the entry form.
These articles from our Wiki give further information on how to do this:
Changing Field Properties
Editing the Entry Form
At the moment, there is no option to add sticky notes or comments in the database like you can in the main text document. However, you should find that the flexibility of the table structure provides you with all the options you need to add your information.
You can link fields between multiple databases, but not currently fields within the same database. There are, though, a couple of other options you could investigate. Using the Organizer, you can select the display colour of the character. So, for example, you could make all members of the same family green. You could also try using the Thinkboard to create a visual representation of the character relationships.
Hope this is helpful