The way
Wrye Bash works is that it maintains a list of tags for each mod (which the authors themselves provide), and these tags contain information about compatibility and load order, like Gameplay mods will go after Graphics mods, etc. Mods can additionally include a list of known incompatible mods (both in terms of strict incompatibility, and which mods have to be loaded before/after the relevant mod), which Wrye Bash will warn you about. It's a clever system, and allows it to maintain and organise lists of hundreds, if not thousands of mods by essentially making mod authors responsible for maintaining their own compatibility information.
But I agree with ZB here (ZB and I agree on something? GASP!!!), this is not worth the effort. Due to the nature of DML, "load order" is, most of the time, not really relevant unless multiple mods are editing the same properties on the same objects, and if they are, you're likely to run into issues regardless of load order, because one of the mods is going to have issues. This becomes even worse with Strings files because one mod is going to break another mods strings, there's nothing that can be done about it. The only other relevant compatibility note is that, if you're using Alarming Cameras and RSD together, you need to use the Alarming Cameras fix that was shipped with RSD, which contains the strings from both mods combined into one file.
I would support some work being done in the mod manager to allow it to detect conflicts between mods by analysing DML, but it's also probably not worth the effort unless someone decided to take it on as a personal project or whatever. That said, if someone is going to be working on mod compatibility in the mod manager, it would be much better if they could add
better string file compatibility, because that's an issue right now and will only get worse over time as more mods include modified strings.
In general, gamesys mods go at the bottom. SCP, and Secmod are the only really relevant gamesys mods right now, as most other ones are deprecated. Then Obj Fixes and SHTUP (and Portrait Fix if you're using Secmod, unless it was included in a recent version I don't know about). Then map mods, the only relevant example is Rickenbacker Automaps, which was made obsolete by SCP 5 but is still useful for SCP 4. Then everything else.
If you're looking for a mod-list that mostly works well together and has a lot of compatibility, I made a guide which you can read
here. I'm not sure if it's all in order for SCP b6, although I did update it for SCP b5 so it should still mostly all work.
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