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I just got a box of pathfinders and i am wondering if i should use ion rifles or rail rifles for the special weapons? If so what should i shoot the rifles at

There is a few ways to play it

If you are taking them for markerlight duty dont bother with the special weapons.

If you are going to use them for damage/emp and whatever, it depends on the target. rail rifles are great against elite targets and possibly side/rear armors of vehicles. Ion are better for light/med tanks on a pinch and better to put a few wounds on high T targets and overcharge encase of wraiths.
Ether way though pathfinders have weak sauce BS and the range isnt toooo great. probably best to outflank em into range (though it can easily be out played) or infiltrated for an attempt at first blood (IIRC i dont remember if they have infiltrate)

They do not have infiltrate but they do have scout.

I kit mine with marker lights and use them to light up the enemy.