What are the drawbacks of deploying a website using the Eclipse IDE?

I started my journey into web applications about three years ago and I'm happy to say that I've finally deployed a working website. My concern is that to deploy the website I use the Eclipse IDE and a Tomcat webserver. So basically I right click the project in Eclipse and then choose "Run As > Run on Server" and then select the Tomcat server I downloaded - from that point on the console spits out some startup messages and my website is online and ready for use. What are are some of the drawbacks of deploying a project this way. I've read just briefly about WAR files and adding them to Tomcats Webapps folder but I could neither get that working nor did I understand completely the process...so is it acceptable to just deploy the project the way I have been doing thus far by running it in Eclipse?