This question was recently addressed under the topic of Spatial Format (dated May 27). Here is the reply that I gave:
The text shown in italics (to the right of the expressions) are what we call "author comments". They are usually brailled on the same line following the expression to which they refer. Transcribers often enclose these remarks within parentheses. An explanation should be included on the transcriber's note page of how these are handled in braille. I think this is the best solution, however it is not the only one. Some transcriber's take these comments to a new line. Others key them when they will not fit on the line.
I cannot point you to a rule for this type of format, and the opinions vary of how it should be done. Once you have established a format, just be consistent with it!
I'm sorry that I cannot give you a more definitive answer. Some agencies have established guidelines for things not covered in the code. If you work as a contract transcriber you could check with your agency to see whether or not they have any guidelines or a specific preference for how this should be handled.