Yes, it can make a difference to run two PCV's, one on each side. It can also help to put on a larger diameter hose on the PCV. You will also want to make sure the PCV screen is still there (under the PCV on the back of the intake) as it helps remove oil misting.
The problem is that the stock PCV line does not flow enough to allow proper ventilation when you start modifying the motor. When there is not enough flow, pressure in the crankcase increases and the oil begins to "mist" in the blow-by gases. This is evident by oil gathering in your intake and in the PCV hose. The more oil you are seeing, the higher the crankcase pressures are, and the more likely it is that you are about to blow your bottom end to pieces.
If you are just using a filter instead of an actual PCV, that's fine too... You're just releasing tons of hydrocarbons into the atmosphere. Just don't let Al Gore find out.