As for I-94, it is normal that you can not find it at web site. It is not necessary to used one when you enter USA. If you have changed status, or renew/extent visa within USA, you should have new I-94, it is part of the approval notice (in its bottom), so just use that new I-94. You just need make a copy of approval notice and notarize it.
For I-485 submition, it need not packed with holes, just order the materials according to the order listed in the "contents" sheet. But if you submit I-485 together for your spouse and/or child, pack the materials based on each person. for example, if you have 3 members, arrange your materials into 3 packs, just stack each pack with a "QU-BIE-ZHEN" is enough. But if same document consists more than one sheet, you should stack them together. For common used documents, you can pack them to an independent pack.