How you use them depends on who you are playing against - target selection is important. If the opponent has big blocks of relatively soft troops, elves, empire state troops, marauders, etc. Then the salamanders are used to strip away ranks (essential for units that rely on being steadfast) and force panic tests. Remember that templates now hit every model touched, which means you can hit a lot of guys in a big unit. Once that unit (which is hopefully much smaller) finally gets in combat the salamandrs can be used to get a flank or rear charge and force a fear test (don't do this if they are still steadfast.)
The other use is to go after high value targets like empire or bretonian knights that depend on armor instead of toughness or even trolls or other units that have regeneration.
Finally, they can take on soft units like skirmishers, fast cav and war machines (but be careful, they can have a hard time winning combat, even against relatively soft units and will often break without the general near by)