For most mods, the author will usually tell you in what order to place it. For example: most of TJ's mods over here will do best if they load
after anything Pescado makes. Read the docs coming with the mod, to find out!
For many other mods/hacked objects, some people may have already found out which order works, and which not. You'll quickly find out by asking around. Usually, the first person to ask, is the one who created it

In the rest of the cases, it's indeed a question of trial and error. That's one of the reasons why one shouldn't install too many hacked objects in a single round... Add 2 or 3 (or maybe half a dozen), try to run the game and see if all works out, then if it does, add some more... If you were to add like a score objects, how would you ever know what to change when something didn't work, right?
Of course, all this is only important when HCDU (Hack Conflict Detection Utility, found at
SimWardrobe) notices that two hacked objects/mods make changes to the same part of the program. One will have to choose which mod's functions are most important to them, and make that one load last.
Hope this helps. Happy simming.