I've got no idea whether flavouring particles are mentioned in the lessons at some point, but the German texts in the translation section are full of them. In case you've ever wondered why the literal translation of words like "ja", "doch", "halt", "aber" and "mal" sometimes doesn't make any sense, have a look here: http://coerll.utexas.edu/gg/gr/mis_04.html
Although I know what these words mean, it's still not easy to translate them. :) I sometimes leave them out and sometimes paraphrase them, e.g. "Ich habe ja schon geschrieben, dass..." -> "As you know, I've already written that ...". It would be interesting to know what professional translators do in such cases.