Alright by searching around I was able to have everything up and running and it doesn't seem to be in conflict anymore, I had to uninstall Anaconda, reboot my computer and then reinstall it after my installation was broken though.
As long as packages and dependencies weren't messing around with each other, I was able to install lightgbm, folium and catboost in the regular (base) environment and use them. Those were installed straight with conda install -c conda-forge packagename, except for catboost which I linked. Do not forget to check for the different versions of conda, python and pip (wheel) which might affect your system.
Also, conda install nb_conda was installed to be able to select different environments in the Jupyter notebook straight away.
I got this from this helpful post and a mix of the answers below.
Then, when I wanted to install Tensorflow, Keras, theano what worked for me are the instructions in the second top comment in this thread though you should not forget to install jupyter again in the activated new environment you created.
After that, close everything, re-launch everything and in the top right corner of the Jupyter you should be able to pick the different environments and work from there.
I hope this will help someone else in the same predicament.