Solution 1:

The example on Wiktionary uses brackets (http://en.wiktionary.org/wiki/i.e), and the at Answers.com all the examples show i.e. used in parenthetical expressions of some sort (bracket, comma or em-dash) (http://wiki.answers.com/Q/When_to_use_ie_in_a_sentence). So I would suggest it is probably a good idea, particularly if there is some doubt as to where the restatement ends and the rest of the sentence begins.

Solution 2:

More than a few style guide recommend dropping such Latin abbreviations entirely suggesting "that is" instead of "i.e", "for example" where one might otherwise use "e.g.", and so on (not to say "etc.").

But if you are going to use them at all, putting them in parenthetical comments seems fine to me.