Hi there , I just got a copy of CFS3 last year and I'm new to it as well. I've left the CFS1 world and I'm working my way on up in CFS3. For starters I too tried the Avhistory Wepak since i got my game. here's what I went through to get my CFS3 working correctly and efficiently:

1. Re-install CFS3 on your hard drive
2. Go to AvHistory.org and download the Wepak and all essential files from the tools section (be careful not to delete anything from anywhere in CFS3, trust me I've done the research!)
3. Create new folders to store the Wepak information in the base folders in CFS3 (example: main folder :Weapons, subfolder:Shared weapons; Main folder:pylons, sub folder:pylons)
4. Make sure you dont delete anything from the base folders like Weapons,pylons, effects or anything like that)
5. Download all Ground crew addons and place them in the Aircraft folder and download any other ground crew addons so that they mesh with the CFS3 main folder( this is especially helpful when you get German bombers like the He111 or Bf110 series)it helps the game run more smoothly. Also when it comes to the AvHistory preload and effects files ,replace the original ones in the Default CFS3 directory.
6. Download and run the BDP nuker from Avhistory. This will clean up your hard drive and enable all Wepak addons to be used in CFS3 gameplay. The effects are amazing. I hope this helps you out.

thats it. Just follow the steps and it will become much easier. If there is anything you want to know remember you can use your PM.

Have fun when youre done

P.S. Be careful when downloading Aircraft from Avhistory. I got a Spit Mk 14 and when i started CFS3 and selected weapons loadouts my game crashes for some odd reason. It happened to me with my fw200 condor and B-29. Its safer for you to shop around at Simviation Flightsim or Netwings for your Aircraft, missions and tools. CFS3 is veeerrryyy limited in the Aircraft department, so choose addons that really look and perform well,  they help keep the heart up when you get them.