There is quite a clear distinction between the two and no reason at all why you cannot have both as they both perform an entirely different function. Generally a familiar is a physical creature, often a pet of the witch. Historically the familiar was said to house the spirit of the witch, but more commonly these days a familiar will refer to a companion of the witch, likely one with a close emotional connection and possibly one who assists with magic.
Animal spirit guides (sometimes referred to as totems) relate to a mental rather than a physical companion. The spirit guide may have qualities that an individual either aspires to or finds solace and support in. A spirit guide may have lessons to teach and friendship to offer. A person may have several different spirit guides in a lifetime, learning different things from each of them. Usually, you can discover your spirit animal through meditation.
Image http://www.sxc.hu/browse.phtml?f=view&id=1386345 (echiax)
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