ProQuest does not provide specific guidelines for citing EEBO, but does provide a citation tool.
What is the difference between Early English Books Online (EEBO) and EEBO-TCP?
"Simply put, EEBO is a commercial product published by ProQuest LLC, and available to libraries for purchase or license. EEBO-TCP is a project based at the University of Michigan and Oxford, and supported by more than 150 libraries around the world.
EEBO consists of the complete digitized page images and bibliographic metadata (catalog records) for more than 125,000 early English books listed in Pollard & Redgrave’s Short-Title Catalogue (1475-1640) and Wing’s Short-Title Catalogue (1641-1700) and their revised editions, as well as the Thomason Tracts (1640-1661) collection and the Early English Books Tract Supplement. With EEBO alone, you can search for a book based on the information in the catalog record and you can flip through or download page images in TIFF or PDF format. With EEBO alone, it is not possible to search the full text of a book or to read a modern-type transcription of the text.
EEBO-TCP captures the full text of each unique work in EEBO. This is done by manually keying the full text of each work and adding markup to indicate the structure of the text (chapter divisions, tables, lists, etc.). The result is an accurate transcription of each work, which can be fully searched, or used as the basis of a new project. To date, EEBO-TCP has produced more than 40,000 texts. The EEBO-TCP text files are delivered back to ProQuest and indexed in EEBO, so users at partner libraries can seamlessly perform full text searches and view transcriptions right within the EEBO platform, although the texts can also be accessed in other ways. EEBO-TCP is administered by the University of Michigan Library, with teams of editors at Michigan and Oxford."
The above comes directly from the FAQ page on the TCP website, which you can view here.
Early English Books Online (EEBO)
Early English Books Online - Text Creation Partnership Tutorial