I suppose that each time you apply a patch, this latter returns the data at the beginning and modifies the corresponding bytes.
Or otherwise some patches are overwriting bytes on the same offset.
In you case I would take the time to copy the byte sections from the patches to the modified rom manually.
It would be easy to know which bytes are by comparing the patches to the original rom.
Since you want implement a lot hacks that will take some time.
Think this tool will help you to save some time.https://www.romhacking.net/utilities/1038/