While it is possible to have a single term set for your entire organization, you'll probably want to configure multiple term sets—perhaps each restricted to a certain business group, agency, or department. A group is the security boundary for term sets. Here are some tips for managing the term store structure that gives you a good balance between flexibility and structure:

• Use term store groups. While you may have global term sets (such as general business terms, department names, or other topics that are common across the enterprise), you also may find that departments or business groups have specific terms related only to their area of the organization—such as finance, legal, or human resources. You can use groups to organize term sets.
• Use term set hierarchies. Terms can be placed in a hierarchical fashion (such as Books > Cookbooks > Italian or Construction > Materials > Roofing). Well-designed hierarchies will help users to refine data more specifically.
• Be careful to understand the difference between copying, reusing, and pinning terms: 
  • Copying a term means you are using a source term as a template to create a target term. As soon as you save the new term, it is its own entity and is not connected to any other terms.
  • Reusing a term means you are creating an editable linked copy of it in another term set. If you later update the term (either the original or the copy), both terms get updated. This can be both useful and have unintended consequences.
  • Pinning a term means you are making a linked copy of it, but the new term is read-only and can't be changed. This might be useful if you want to create standard sets of terms across your enterprise.
• Establish processes for handling the deprecation of old terms as your business changes.
• Use the Other labels property of a term to add synonyms to it rather than creating the synonyms as new terms. This will help to reduce confusion and keep content labels consistent (that is, rather than creating the separate terms for lawyer, counsel, and attorney, create one term for lawyer and then add the synonyms counsel and attorney to it).