I usually just hand edit the files. You will be concerned with the X, Y and Z axes of your gun positions.
Go to your DP file for the airplane and you'll see something like this:
[GUNSTATIONS]
; FF/ M 20mm Cannon
gunstation.3=1,46,2,0.115,600,2,0.05,740,4,40,1d1*46.3, 2.035,-0.310,1.050,-0.58534,0,-0.35122,0,0,0,0,14.323
It's all the data on the weapon. Each MG or cannon should have a data line like the above. This is the data line for the 20mm cannon in the right (starboard) wing of an Me 109, similar to your plane.
Look for "1d1*46.3" in the line. That is the damage die for that weapon. Not important here other than the X, Y and Z axes for the weapon's muzzle follow it. We are interested in the vertical component, so go to the second entry following the damage die and you'll see: "-0.310" Your planes is probably different. The negative number in this particular DP indicates the weapon is below an imaginary point in the plane. For your plane, just adjust the number down until you have your muzzle flash and smoke coming from the muzzle of each weapon.
When adjusting, I believe that you can make the adjustment in the DP file while the sim in open, but on pause. After the adjustment, un-pause, click on "Change Aircraft" and then select your aircraft again. Once it is reloaded, your modifications will be in effect. I also do this while the plane is parked on the ground for ease in seeing the muzzle flash.
Next step will be to zero your weapons in your 2d panel and then in your VC to your satisfaction. Every good marksman does this with his rifle, pistol or airplane. When you're ready, post here and we can go through that too.
Here is the difference in between -.233 and positive .233 in the vertical entry:
