Solve your model in lyx.
I tried using the paper and pen method when I first set about to solving models.
But I would inevitably lose a page or not be able to read my writing.
Lyx allows you to write latex equations in real time which makes it great for solving models by hand.
I use a text editor to write my papers,
but I copy and paste my equations from lyx directly into the latex file in the text editor.
Write code with a text editor like atom or Visual Studio Code.
Use Skim as your PDF viewer, it syncs up with text editors quite nicely for viewing latex files.
I still use Adobe Acrobat for presenting Beamer slides because the transition between slides is smoother than Skim on my mac.
Use git.
Version control is a lifesaver and prevents you from having 20 different files all trying to do the same thing, 19 of which you don't need.
Bitbucket provides private and free git hosting.
Sourcetree provides a nice GUI for git allowing you to avoid using the command line, if terminal is intimidating.
You can also link up Sourcetree with your GitHub and Bitbucket accounts.
If you don't have a project idea yet, duplicate a paper.
Email the author and ask for their data and code, assuming they are not using proprietary data.
I recommend translating the code to another language.
This will force you to understand each line of the author's code.
Come up with an extension to the paper at the very least.
Save everything! This includes notes of other grad students and your classmates,
slides of all the classes you have taken or taught etc...
You never know what class you'll be asked to teach or what you'll be interested in researching in the next five years,
and the less you have to reinvent the wheel the better.