Other than removing the shifter, there's really no difference in pulling an engine with a manual instead of an automatic. You CAN remove the transmission and bell housing, but there's no need. If you do, there's no need to pull the clutch. Normally, the pressure plate-to-flywheel bolts are standard hex-head, but they could be anything: Torx, spline drive, allen socket, double-square, double-hex, etc. I suspect you're looking from the bottom and seeing some part of the pressure plate, NOT the bolts holding it to the flywheel. You don't want to unbolt the pressure plate from the flywheel until the trans/bellhouing is out of the way.