I would say it is absolutely essential that you write what you see, and do not be tempted to update anything to 'modern' spellings. In an ideal world, if you are entering these details onto a database of somesort, you would have an additional data field 'modern spelling' so that searches for the modern spelling produce results on the alternate spelling too. If you are transcribing, then all you do is copy, if you start to 'correct' things as you go you get into an awful pickle, as eventually you get something that you are not absolutely sure about, and you change it, only to realise much later that you were wrong to presume that Ballakeog was Ballakeig or something, and then all your clean data is tainted. It might also be a good idea to have another data field in which you enter a number or letter or something to indicate that there is some doubt as to the reading of the original. That might allow either someone else to go through and double-check just the doubtful entries, or other researchers to double-check a particular entry if they wanted to.

Good luck

David