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I've been wracking my brain over this one. i've watched so many here lately that i can't keep all the titles straight.

At the beginning of the movie, there is a boy running through the woods trying to get away from something then it fades to the present time.. a family moves into a house that belonged the man's father or uncle. The architecture is really wierd and turns out its layout is based on some symbol for the cult,  naturally its haunted. go figure. the little boy starts getting marks on him and when he's in his room by his self, the toys come on on their own. years ago the cult was at the house and they were murdering children for sacrifice but one got away and things went wrong. the father starts going crazy and digging a giant whole in the living room floor. Someone goes to the uncle/grandfather for help but it turns out he's behind it all and injects them with something

Sounds like Darkness.

http://www.imdb.com/title/tt0273517/

Could you be thinking of the 1987 film "The Believers" starring Martin Sheen?  The plot you described sounds very similar to this movie.

Plot:
"A police psychologist and his school-age son become embroiled in the machinations of a mysterious cult religion in this thriller from director John Schlesinger. After his wife is electrocuted in a freak accident, Dr. Cal Jamison (Martin Sheen) and his son, Chris (Harley Cross), move back to Manhattan, where Cal went to school. When not spending time with his son and surrogate extended family -- husband-and-wife anthropologists Kate (Elizabeth Wilson) and Dennis Maslow (Lee Richardson) -- Cal settles into his new job and romances his landlady, Jessica Halliday (Helen Shaver). Soon, though, a series of brutal murders of young children begins to take over Cal's life. Through the ravings of policeman Tom Lopez (Jimmy Smits), who believes the killers have supernatural power over him after stealing his badge, Cal learns of Santeria, a voodoo-like Latin American sect that mixes elements of Christianity and pagan mysticism. Although the religion turns out to have ties to some of the richest men in the city and even Cal's well-meaning maid seems to be a practitioner, he can't get any straight answers as to whether the cult is responsible for the murders. But after a sinister African shaman (Malick Bowens) places a curse on Jessica, Cal finally begins to understand the danger that faces him -- and his son. The Believers was very loosely adapted from Nicholas Conde's 1982 novel The Religion." ~ Brian J. Dillard, All Movie Guide