New To Sentora - Help Installing Software After Install

So, I am a long time user of cpanel, but since I have decided to finally ditch shared hosting and build my server from scratch using DigitalOcean VPS services, I thought I would look into what was available as a free open source control panel...so far SENTORA has been the best out of the 5 I evaluated. 

Now I got my websites up and running on Sentora and DigitalOcean, but I am a bit worried about adding software through Ubuntu's apt-get. Should I be?

For example, I want to install image-magick. I went ahead as I normally would and ran 

# apt-get install image-magick. 

It installed just fine and now I have it running and working with my Drupal sites. But did I break anything in Sentora by doing this?

If I want to install other software on the server box such as htop or something else. Do I risk breaking Sentora and causing outages for my websites being hosted?

Also, when it comes time to want to upgrade php to a newer version, is it safe to run the apt-get command to upgrade php, etc, or should this all be done through the Sentora control panel?

Just curious how I am supposed to treat this server now that Sentora is running on top of it and managing things. 

Thank you!