You can stack patches on games but how you might set about it, especially if pokemon is the game, varies a lot and depends upon a lot of factors. I assume the trainer mod is actually a graphics mod rather than a force to another character in the game for this. If it is a force then depending upon the method used (for my money there are three, maybe four methods of setting about it) things change a bit again though possibly for the better assuming you are or can get the help of someone that knows how this sort of thing is done.
Xdelta is not a DS aware patching format (other than ones that deconstruct the game, patch the individual files and rebuild it the only format that is DS aware is dps which was pretty much only used for Jump Ultimate stars and basically does the same thing from the first part of this bracketed text) so while it will attempt to change data locations if it detects a shift it is not going to be aware enough to patch the already changed file if things have shifted. Similarly xdelta does have a file to be patched check to make sure the would be user is using the right version. I do not know what the GUI programs do about this though you can manually override it.
If the trainer change does it all in place, does not shift anything around and does not change data to be changed by the difficulty patches then do the trainer patch and then the difficulty one which I imagine will change quite a bit. If it does change things around you are not out of luck yet but you may have to play minor league ROM hacker.
I do not know if HG "sprites" are in fact 3d models (the game itself uses 3d extensively if memory serves, at least I think it was that one for first person pokemon) but either way your job would be twofold
Patch the trainer mod in and see what files are changed. Various ways you can set about this (personally I would hope the game is not shuffled around too much and then compare differences between stock and patched and figure out the differences there, if you want to deconstruct it and play with the fc command you are free to do that too) but once you know what goes then that is good.
Take a fresh copy of the original ROM and patch that with the difficulty mod. Deconstruct the ROM and replace the files you figured out were changed, this should do it. If the same files were changed in both hacks you now have to figure out what goes and how to merge them, if it is a binary hack it might not be too hard and there are a whole long list of ifs for this so I will leave it there for now.
Short version
Try applying the trainer mod and then the difficulty patch. If that does not work and you can not get a handle on what you might need to do next (
http://gbatemp.net/threads/gbatemp-thoughts-and-links-10-feb-2012.320568/ should get you started) then report back.
