I track the weapons skill separately, using the granular rules described on page 258. Players can have different skill levels in different, but similar weapons which are tracked separately and accumulate experience separately.
Think of it this way...
Blaster has a 15% base.
Laser has a 20% base.
At character creation, you decide to put 100 points into those two skills, split 50/50
Blaster becomes 65%
Laser becomes 70%
Later in the game, you use the laser and get an experience check. You succeed at the check and gain 6 points.
Blaster stays at 65%
Laser becomes 76%
If I used Weapon Classes, which it looks like you're doing, I'd decide on a base skill for Pistols, Energy and add skill points to that instead of whatever is listed for each individual pistol. Then, regardless of whichever type of Energy Pistol my character picked up, he'd have the same rating.