If the co programs are causing corruption it’s probably because of bugs in their code. Not much you can do about that. The more common reason for corruption is mistakenly loading a .DO misnamed to BA from disk.
As far as space, for small co’s you can keep them as a co file in RAM. For large ones consider dedicating a REX RAM sector. Poke load or load and CLEAR for your co, save a tiny trigger file, and delete it from the RAM disk. This will give you maximum free ram / ram filesystem space. This was a great way to run TMPC which is huge. For loading from disk, it may be that you are using an incorrect CLEAR statement before launching. Normally if you forgot to clear the machine should just beep at you when you run the co. But if the co has bugs it might depend on a special CLEAR statement that goes lower than its load point in RAM. — John.
