Provide them separately. They rarely convert successfully when embedded. Today's word-processors have many useful features for document layout. They invariably conflict with the lay-out process and take effort to undo. If you wish to use endnotes or footnotes, particularly if they are to appear at the bottom of each page, provide them at the end of your article in plain text and inform the Editor accordingly.
Graphics are more than acceptable, both in electronic form and as paper.
Again, if doubtful or unsure contact the Editor. This protection extends for some years after the author's death. It extends to illustrations as well as words. This is not very precisely defined, but it may depend on how much of the copyrighted material is used, and in what way. Ideas are not themselves protected by copyright.