The proper way to lower a vehicle, without terribly adversely affecting the alignment angle of your suspension is by using a suspension lowering kit. What a suspension lowering kit includes will depend on how much lowering is to be done, what kind of car and suspension is being lowered, and which end of the vehicle is being lowered. Most front ends can be lowered by using a drop axle front spindle and shortened and stiffened coils on shortened shocks or struts. Most rear wheel drive rear suspensions can be lowered easily by installing lengthened shackles that connect the leaf springs to the frame, or by mounting the axle under the leaf springs and/or on blocks.
For more info, see 5 Tips for Buying a Lowering Kit