Any module that was engineered under the old system needs to be converted to the new one before doing any additional engineering to it, this includes experimental effects.
Generally, if you have the time and incentive and do fly the Anaconda into combat often, I'd suggest to actually convert and G5 all of your modules (or engineer new ones from scratch), since the result is almost always superior.
Can't say much more about your weapons loadout, a healthy mix of lasers and MCs is always a viable combination for PvE though. Which engineering to choose depends more on your playstyle and the ship you're flying, but generally, like I said, (projectile) weapons with travel time are increasingly prone to miss over longer ranges, and the damage of a shell with an increased (falloff) range is still zero if it doesn't hit. I'd even say in most situations overcharged is the way to go for MCs, but YMMV. Same goes for the Autoloader experimental, you only need Corrosive on (a small) one and I'd only use Incendiary if I had no additional thermal weapons fitted.
With the lasers you should experiment a bit, for example, I like a mix of turreted long range medium pulses or bursts (to deal with the small fry), and large efficient/thermal vent gimballed beams on my capital ships.
You know
coriolis.io? It's a great site to plan your ship builds.
And for finishing off large opponents like other Anacondas, try sub-targeting the power plant, the huge MC will take it down in no time if you manage to get your angle right.