Pedigree Forge has two levels of configuration:
Settings that apply to the current project only. Access them from the Project Settings panel (click the cog button near the lower-left of the main window). Examples include source transcript markdown, default place formats, and report preferences.
Settings that apply to all projects. Access them from Tools > Options. Examples include the name-entry mode (separate or combined fields), embedded browser settings, and spell-check options.
Some options are covered in other sections of this guide — the relevant section will note where to find the setting.