I have a custom table in MODX database set up and working, thanks to this article: http://bobsguides.com/custom-db-tables.html and now I need to add new column to this existing table. How can I do this the "MODX way"? Or do I have to create the component from scratch again?
You can manually add the new column to the database, then update your xml schema and map files to include the new column metadata. If you have a build script you could simply run it again after amending the schema to regenerate the map files.
I could be more specific if you paste in your existing schema and description of the column you want to add.