I found the biggest thing with taking on an Anaconda especially if your gradually progressing your ship and loadout and are on a limited budget is confidence!
Sounds a bit random but here me out, I found that I would drop in on a kill mission and try and manouver around him to get behind where his weapons could do the least damage but I would never get near enough to get in close as he would have my shields down before I could get close. I tried this in an Viper, an Cobra and an Asp all with the same result, getting battered with out really making a dent on him.
Once I had a bit more money and I was not so paranoid about loosing my ship I started to get a bit braver and just immediately boost towards him and get in behind him, I could then actually start doing damage to him while sometimes keeping in the fight long enough to get his shields down and even if I got hammered I could time my break off to get away with out to much damage
Once I was confident that I could actually live with the beast for more than a few seconds then I started to experiment with chaff (really useful) and gimbled weps and also a shield cell once I could afford it.
As the rest of the guys have said targeting the power plant or other critical systems really helps speed the process up but you still need to get in there with enough shield left to be able to stay in the fight and that comes down to the confidence thing