Kissyalove14 I would always test .package files unmerged first. A batch of 50-100 isn't going to drag down performance in a noticeable way, at least not when the individual files are fine. And if you do see a problem, you'll want to be able to split and re-test without having to track down the original files. I would only merge files once I'd confirmed they all worked separately.
And by testing, I don't just mean having them in your game, although that's a good place to start. You can't really know whether a cc item is fine until you use it in-game and nothing bad happens. That means placing objects and having sims wear any clothing or hair.
If you want to be thorough, I would also suggest allowing a baby to be born as you test, because some bad cc is fine until it sticks to a baby and gives it a Grim Reaper robe or a centaur body or whatever. You can use NRaas MasterController's Instant Baby command, or have a test save where a sim is about to go into labor and play through until the baby is born and is confirmed to be intact.
For content that's already merged, you could test one merged file at a time as long as you were sure to test each and every item it contained, as in, placing the objects, and assigning the CAS parts and forcing sims to display them. While it's better to test before merging, you might at least be able to find a single merged file that has a problem this way, and then only need to track down the originals from this file.