Anything that made it into the primary will drop to the bottom and be left behind when you transfer to secondary. Nothing to worry about. The particles were probably just hops and some proteins from a cold break while you were chilling your wort. Some proteins actually need to get into the primary for fermentation so you're good. SOme people use a strainer and funnel (if going into a carboy) and pour the wort through that but I prefer the whirlpooling method. I usually stir it once it's cooled and let it sit, covered, for a good 15min then put my auto siphon in the corner of the pot sitting a little higher than the stuff at the bottom.
"So we were slammin' beers in the church parking lot..."
"I'm much too young to feel this damn old"