I have done quite a bit of research on the (legal) use of photocopies for performance and examination over the past few years.
Until 2012, it was necessary to have permission from the publisher for a photocopy to be made, even if it was solely for the use of the examiner. The MPA (Music Publishers Association) has a Code of Fair Practice that lists specific situations in which it is permissible to make photocopies. This was, in my opinion, ambiguous when it came to making copies for examiners: copies made for the purpose of an examination [by someone setting the exam] were included, but interpretation varied between boards as to whether this included copies made by candidates for the use of the examiner. Accordingly, until recently the ABRSM followed the policy that candidates must obtain permission before making copies for the use of examiners. Given that, to the best of my knowledge, publishers always granted permission for this purpose, it seemed to me that the whole process was wasting the time both of the candidates and of the publishers. I brought this to the attention of the MPA, who accepted my point and undertook to review it with their members; and it is gratifying to see that the 2012 edition of the Code includes specific permission for candidates to makes copies for examiners provided that a copy of each piece is owned by the candidate, copies are appropriately marked up and copies are retained and destroyed by the examiners after use (see www.mpaonline.org.uk/sites/default/files/Code_of_Fair_Practice_1.pdf "Permissions", item 10).
A long as your music is published by a member of the MPA (and it's very unlikely that it's not), this deals with the permission side of things. As far as pencil marks are concerned, that's up to you. Personally, I'd make sure that any copy is clean with the exception of anything you specifically want to include (e.g. if in your performance you intend to depart deliberately from what is printed it might be wise to annotate this so the examiners have in front of them what you actually intend to perform).
Presentation is, again, up to you. I copied everything onto double-sided A3 and presented a folded & stapled A4 booklet containing everything in performance order and a folder would also be absolutely fine (as long as you don't mind potentially losing it to the examiners). Although I don't believe the way in which you present the printed music is included in the marking criteria, it would be wise to ensure that what you provide and how you provide it is easy to use (e.g. use index tabs to locate pieces in larger printed publications, and make page turning easy for photocopies). I would say a staple in the top left hand corner would be just about ok, provided it's single sided (so the examiners don't have to turn copies round or over), but it's borderline and may seem slightly unprofessional given the context. Fundamentally, you want the examiners to concentrate on your performance and not to be distracted or irritated by trying to find or to follow the music you are performing!