With the prevalence of firearms and artillery, it seems to me like dense formations of pikemen would be slaughtered on a battlefield in the late 1600's. My question is: How would a typical commander of the time deploy and utilize his pike infantry effectively?
By the time period in question, the pike blocks (not phalanxes) have taken further and further secondary roles to shot/firearm troops.
In the early 16th century, the shot troops are there to support friendly pike blocks and harass enemy pike blocks when contact is made. By the 17th century the proportions have changed drastically. A figure from "Fighting Techniques of the Early Modern World" shows:
You can guess where the trend was heading. Swedish infantry in the 30YW deployed about 1-1 pikes-muskets, and this isn't much different from what the Imperial and Spanish troops deployed, even if the Swedish ran smaller squadrons than their adversaries.
By the 1650s period, the pike block was a smaller contingent with muskets on both sides. Or rather, perhaps it is more accurate to say that an infantry squadron was a 6-deep line of muskets with a few pikes concentrated in the center. If that squadron is threatened by horse, the pikes then move forward and muskets back behind them to get protection.
You may want to read through previous answers on pike and shot formations in battle.