The first step is to remove the automatics skill:
Go to the Skills: Active tab in the editor, press "New (Copy)", and find Automatics in that list - write down the unique Id that's in parentheses (skaAutomat), and cancel out of that list.
Next, go to the *Hidden tab, create a new entry, and fill in the unique Id of Automatics.
Go to the dicepool helper tab, and press "New (Copy)", and find each of the skill specialties that used to be for automatics (Assault Rifles, Carbines, Machine Pistols, and Submachine Guns). Write down the unique Id of each on a piece of scrap paper. Now, the same way you used the *Hidden tab to remove the automatics skill, remove the specialties for that skill.
The second step is to alter the Firearms Group so it no longer contains automatics and now contains heavy weapons:
Go to the Skill Groups tab in the editor and press "New (Copy)". Choose the Firearms Group, and while you're in that list, write its Id on a piece of scrap paper (skgFirearm), and press "OK". Now, enter a new unique Id for the copy along the top (like skgFirearA), and on the right-hand side, find "Replaces Thing Id", and enter the original Id there. Now find the "Active Skills" option in the center section. In that list, un-check Automatics and check Heavy Weapons.
On the Skills: Active tab, press "New (Copy)", choose "Heavy Weapons", and again, write down the Id on a scrap of paper. Like the Firearms Group, you'll want to give this copy a new Id and set the "replaces thing Id" field. Then, in the center section, choose "Firearms Group" for "Skill Group".
The third step is to re-direct all of the skill specialties for automatics to other skills:
On the Dicepool Helper tab, press "New (Blank)", and give your specialty a name and Id. Set "Skill" to "Longarms". For "Weapon Categories", select all the specialties that used to apply to the automatics skill. (If you wanted machine pistols and maybe SMGs as pistol specializations, you'll need different Dicepool Helpers for each of those skills, each tied to the right weapon categories).
Sorry I didn't get back to you sooner, I was at the PaizoCon convention in Seattle last weekend, and I'm still catching up on emails and forum posts from that period.