When your professor or TA says, "Don't use encyclopaedias to write your paper," what they mean is that they want you to focus on using primary (journal articles) and secondary (books) literature to write your assignment. However, reference books can still occupy a very useful place in your research process.
A reference book is a good place to begin your research when you know very little about a topic. You will probably not cite the encyclopaedia or dictionary but in may provide that small piece of information to get you going on your topic. For example, if I need to find information on the organism Balanus, where am I going to look? By consulting a reference book first, I can figure out that Balanus is the scientific name for barnacles, sessile crustaceans that live in the ocean. There might even be a picture of the organism. This information will help me when I start to look for more information in books or journal articles.
You can find reference books by using Summon. After typing your keywords and searching, you limit your results in Summon to just reference books. Under Content Type, click on More..., then select Reference.
Wikipedia is a reference source and it can be used as a good source of vocabulary and references to more academic information. The name Wikipedia describes what it is - an encyclopedia created in a wiki. Wiki content can be authored by anyone and the content found in this source can be modified at any time. Wikipedia is best used to find other sources, rather than relying on it as the definitive source for your academic paper.