Actually, reverse that. [EDIT] : whoops. This was written in reply to Betrayal's post.
(I'll be writing this with the assumption you're a beginner, so that this post will be helpful to complete noobs as well. It also saves me the trouble of trying to guess how much you've already found out.

)
You'll need to find the entry in ships.tbl that has the beams, and find which turrets are using the beam turrets. Example:
$Subsystem: Turret07, 3.0, 1.0
+Default Pbanks: ( "BVas" )
This is all part of the $Subsystem: entry in the ship's ships.tbl entry. It has this format:
$Subsystem: <subsystem name>, <percentage of ship's hull>, <turning speed (if it's a turret)>
+Default Pbanks: ( "<weapon name>" )
The subsystem name ties in to the model file (the .pof file). It shouldn't be renamed if you're modifying a turret. The percentage of ship's hp is pretty self-explanatory, and the turning speed is the time in seconds it would take for the turret to spin 360 degrees.
The weapon name is a reference to the weapons.tbl entry. Big-ship missiles kind of suck and are underused in FS- You may want to give it a Cyclops or Piranha instead of a Fusion Mortar or FighterKiller.
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Well, that's what the info in ships.tbl does. You need to change it. To do this, we'll use an SCP feature made of awesomesauce called modular tables. Basically, <name>-shp.tbm adds on to the ships.tbl, allowing you to put in new ships without overwriting anything.
Another feature tbms have to offer is +nocreate. Basically, you use it to override certain fields in an existing ship. You'd make something like
#Ship Classes
$Name: GTC Fenris
+nocreate
$Hitpoints: 300000
#End
If you wanted to make a nigh-indestructible Fenris.
You'd do pretty much the same thing- use your ship name, "+nocreate", then the $subsystem entries containing the beams you want changed.
Remember to change $Default PBanks: to $Default SBanks: to mount a secondary weapon.
[EDIT] You know what IMO we need? tabling tutorials. We have a few good ones for FRED, some really outdated ones for modelling but modelling tutorials are all over the place- A good, brief set of tutorials for tbl entries would be an excellent primer.