This is a guide for creating a patch for mods that edit the skill perks(Rifleman, Gunslinger etc.).

First of all you'll want to load the Skills Only version of BE along with the mod you want to create a patch for as non active files in the creation kit.

The Main Skill Handler Perk

All of the skills(Minus the crafting skills) are handled by a single perk in BE: the 1BSWeaponSkillsPerk so open that(It only managed weapon skills at first, but I eventually put non combat skills in it).
They do not actually range from 0 to 100, but from 0 to 1(in steps of 0.01) because perk entries only allow entry to 2 decimal places and that causes problems. Dividing by 100 circumvents this.
The ones you see in the menu are for display. They directly influence the skills used in calculations though. So with the skill 1BSRifles, the version you see in the level up menu is actually 1BSRiflesDisplay.

The perks contains entries that manage how a skill affects different aspects of the game(how the Rifles skill affects damage from rifles, how Barter affects buy prices etc.)
For most of them you can simply think what effect you want the skill to have at 100 and change the multiplier to suit(+30% Damage for Rifles would be 0.3).

You can also set entries to only take effect when a skill reaches a certain level. Like with Pickpocket: I made the ability to reverse pickpocket explosives only be available if the player's Pickpocket skill is => 25 by setting a condition to check if the Player's Actor Value 1BSPickpocketDisplay is => 25.

Stimpaks & Radaway

There are a few that are a little more tricky though. The amount healed by stimpaks and radaway has a funny number system. Basically 100% health for Stimpaks is +27.34, and for Radaway it's +273.34. They weren't designed with a percentage system in mind at all.
To get around this I made the equation: Value = Value + (MedicineSkill x 14) when Medicine is less than 100. And when It reaches 100 it uses the equation: Value = Value + (MedicineSkill x 27.34).
Same with Radaway but with 140 and 273.34 respectively.
So if you are going to edit these values you'll need to do a little testing.

Accounting for Perks

When you've set up the skills to reflect the changes in the mod you're patching, you'll need to think about if this mod changes the skill perks in a way that isn't just editing the values of buffs, and create new perks to replace them if they do(Since BE requires these perks to have no effect). For example: Rifleman, as well as affecting weapon damage, gives the player the ability to penetrate armour when using a rifle. So I created a new perk: 1BSRifleman that gives this ability.

As long as you get all these perks then their shouldn't be any issues of compatibility or weirdness in the game.

Reload Speed and Weapon Skill

There is also a script which I use to dynamically change the player's reload speed on the fly, depending on which weapon type they have equipped and their skill with that weapon type.
You can open up the 1BSReloadSpeedAbility Ability to see the different effects for each weapon type(Rifles, Pistols and Heavy Weapons).
They all use different Magic Effects that run the same script: aaaBSWeaponTypeRifleReloadSpeed(Just a name) but with BSSKills property in each of them set to a different skill in the properties menu(1BSRifles/1BSPistols/1BSHeavyWeapons).
This system can be set up to include something like Energy Weapons also. You just have to add an effect to the ability that runs the script with BSSkills set to aaEnergyWeapons(Or whatever you want to call your skill) and set the conditions to check if the weapon is an energy weapon. You'll also need to change the conditions of the other effects in the ability so they exclude energy weapons.
Lastly, open the 1BSReloadSpeedModifier Global. This is the number that determines how reload speed scales with weapon skill. It represents what the modifier will be when the skill is at 100. I've set it to 0.3, which means at skill = 100 then Reload Speed = Base Reload Speed(usually 0) + 0.3.

And that's about it. if you have any questions please don't hesitate to  ask.