Hello Quisheng,
Great to hear you're trying out the native ArcPy project, I'd be happy to help you. It should work for anything that's running inside the conda environment, you'll just need to run the commands inside the activated environment. Here's IPython started this way:
(arcpy-native) arcgis@ubuntu:/$ ipython
Python 3.6.6 |Anaconda, Inc.| (default, Jun 28 2018, 17:14:51)
Type 'copyright', 'credits' or 'license' for more information
IPython 6.5.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import arcpy
arcpy
In [2]: arcpy.GetInstallInfo()['Version']
Out[2]: '10.6.1'
This should also work well for Jupyter Notebooks and tools like Spyder, which can be installed into the environment. The story for other external tools is still a little complicated, the native ArcPy interface has to initialize system environment variables in order to operate. The script that executes on startup is available in $CONDA_PREFIX/etc/conda/activate.d/arcgis-server-10.6.1-py3-env_vars.sh if you'd like to take a look. The simpler way to get this along with your IDE is to start your IDE from within the active environment, so e.g. type `code` after activating the environment to start Visual Studio Code [note: I haven't tested this, but it should inherit the calling environment on creation]. Alternatively, you could create a bash script that first sourced that file. This is necessary because tools that call into ArcPy need to initialize the server pieces internally which are used for their dependent calls. We are looking at simplifying this for a future release, but hopefully that's enough information to get you started.
Cheers,
Shaun