When I place bundles in ./bundles folder, krita will duplicate the bundle to the root, and show 2 instance in the resource manager. If I install bundle from krita resource manager, it just place it to the root. So the bundles folder is not useable right now??
If you at least had told us which version of Krita you use and from where you got it, and of course also named your OS and its version number, we could help you far better. So it is only a shot in the dark…
When your Krita is NOT active in memory, so terminated and can’t be found in your task manager, then you can copy bundles into the folder bundles in Krita’s resource folder. Krita should simply load them the next time it starts without copying them to the end of the resource folder. That is at least the behavior of Krita here on my machine in whatever version of Krita above Krita 5.x I use, no matter if it is on Linux or Windows as the used OS. Krita before 5.x behaves differently because of the different resource management.
Michelist
Hi @yikscloud I’m just wondering why you’re not installing the bundle through the regular import bundle manner in Krita.
Okay, I don’t know the reason @yikscloud may have, but I know the reasons I have for using it. But in common it could be like this:
After a possible reinstallation from scratch - for example, to get rid of old clutter from a previous installation in one go - you may have many bundles to reinstall. However, if you simply copy them all at once into the Bundles folder (or to the end of the Resources folder) instead of importing them via Resource Management, they will all be imported in one go.
And why use the Bundles folder? Perhaps out of nostalgia - after all, before Krita 5, that was the place for bundles - but you can also do this for the sake of organization. I even have subfolders within the Bundles folder to neatly separate the bundles from the “repeat offenders” 
among the brush makers.
Michelist
That works ok, Krita picks those up? 
I thought it would have a problem with sub-folders.
For bundles it never stopped working.
But it is a big can of worms where mainly non-bundled resources (and ancient bundles with subfolders in their resource-holding folders) are affected by subfolders found in the folders of Krita’s resource folder, and even that not under every condition. Mainly when referenced out of a bundle, but that would go far too far to explain.¹ If you want to find it out, you have to experiment yourself, and you have to cope with possible issues yourself and know how to fix them, and sometimes it behaves very strangely and unpredictably.
Michelist
Âą Because I fear it would cause too many support requests from those who have to try everything, understood or not, because they constantly read anything only in part (to explain something like that is a mistake I do not plan to repeat, because I did it once, and non-tech-savvy users meant they had to try what they did not understand and wrecked their systems, but it was another forum, and users shred their router settings).