Is there a step by step detailed guide on how they work and whatnot? I've asked my guild but I am still a bit lost.

Do they add to the stats on the mods in the armor? Do they replace them? I see people with BiS in PvP gear? How or why would they do that and lose the expertise?

Not quite clear on what you're asking.

Generally the grade, rating or level is the best indication of what's best in slot. Black hole is grade 26 for example.

People running around in PvP gear without expertise are probably either one of two types, type one is they are really PvE players but like the look of the armor (or retain set bonus) or type two, they've analysed all the various stats and decided to drop the expertise in favour of something else.

I use Noxxic.com for guidance on what are the best stats for me to have for each character.

Is there a step by step detailed guide on how they work and whatnot? I've asked my guild but I am still a bit lost.

 

Do they add to the stats on the mods in the armor? Do they replace them? I see people with BiS in PvP gear? How or why would they do that and lose the expertise?

You seem to think that BiS mods are a different kind of mod from regular mods. They're not. BiS means "best in slot" and simply means that if you put any mod with different stats into that slot instead, you would have worse stats/performance (going by whichever metrics you prefer).

Any mod you replace is overwritten. Any of: armorings, mods, enhancements, barrels, hilts, crystals, and augments can be replaced.

For example, let's assume that I'm a Sentinel (damage) and I've determined that I've reached the "soft cap" for Strength and I already have my target Critical Rating and Surge Rating. In that case, any new Augments I add should be the purple (artifact) Overkill variety with +18 Power and +12 Endurance. That will be BiS because I get the most benefit from additional Power over any other stat. On the other hand, if I had started filling in Overkill augments first and didn't have any Strength ones, then BiS for the additional slots might be the Might variety with +18 Strength and +12 Endurance.

Expertise has a soft cap as well, which is why people don't necessarily have full Elite War Hero and use PvE mods as well. It all boils down to whether the benefit from one stat exceeds the benefit of another stat. When you equip a piece with Expertise, you can hover over Expertise on your character sheet to see the benefit it gives you. Likewise with other stats. That's pretty much sufficient for defensive abilities (just compare the numbers), but for offensive abilities you will likely want to parse a PvP dummy session and see what performs better. Or take advantage of people who have already figured out the numbers