how to put or handle this configuration and where?

In your clearml.conf on the machine with the agent just add at the bottom of the file agent.venvs_cache.path=~/.clearml/venvs-cache

how to put or handle this configuration and where?

Yes I mean the python packages, I would prefer to have all the installation once and if a new package is used just to install the new package not every time the same packages get installed many times.

I have a question regarding running the code on the remote machine, each time I run the code I see the console in the ClearML server start downloading all the libraries I used in the code and when I run another code the same thing happens so why it has to download all the libraries again and many times?

I'm assuming you are referring to the installation, the downloaded python packages are cached.
You can turn on full caching by uncommenting the following line:
https://github.com/allegroai/clearml-agent/blob/077148be00ead21084d63a14bf89d13d049cf7db/docs/clearml.conf#L116