How to define an SPI connection ...?

Well, you can:

• Just use the Web IDE normally and set save on send in the options, which wraps everything in setBootCode for you automatically. That'd be the sensible thing to do, but maybe you have other reasons :)
  
• Use the espruino NPM package (https://www.npmjs.com/package/espruino) on the command-line. You can make this write code to Espruino, or can get it to write the code it would have written to Espruino to a file, which might be what you want?
  
• Manually download modules from http://www.espruino.com/modules/ and try and put them in manually with Modules.addCached (inside E.setBootcode)), but that just seems a bit crazy to be honest :)