You only need the one copy of the nodejs and mongodb software, regardless of how many different node scripts or mongo databases you want to create.
To create a new node project, you would typically create a new directory named after your project, and in that directory, run the command "npm init", which will interactively walk you through setting up some initial aspects of your package.json file. Later, you can edit the package.json file in your editor as needed. Create new js files in your editor as needed to implement your code. Use "npm install ... --save" to install dependencies that you use and to record them in the package.json as well. Assuming you've set up the package.json file to do this, you would then run your code by running "npm start".