Subordinate clauses can, as mentioned by rhyaeris, be put inside parentheses. This is useful if you want to allow the reader to be able to skip the information within the parentheses.
However, there are many ways to structure a sentence in Japanese, and depending on media, some might be more suitable than others (think: some media call for more formal writing; speaking and writing are different; etc.) Depending on the length of the sentence and number of clauses, you might not want to use parentheses at all.
Are commas still appropriate, and where in the sentence should I put this?
Yes. They are not always necessary, but if you decide to use them, you should place them to separate the clauses.
Here are some examples on how you can phrase the example sentences without using parentheses:
Tanaka-san is, for obvious reasons, a good person.
He took the train to work, as most people do.