Hey there Holister, the Thompson Chain reference Bible is fine, there is nothing wrong with using it, it is more of an aid to compare and search rather than study, although in this electronic age, we can use a much better study aid called
swordsearcher which has the Thompson Chain reference topics within it.
The Scofield Bible is fine as long as its the "old" Scofield. As Brother Bones said, don't get to caught up with "study" Bibles, there is nothing wrong with them of course, but then the study would be someone elses thoughts, not your own.