Should references in the supplementary information be included in the main text? I have been cutting some sections out of my article and moving them into the supplementary information section so my paper will fit within the journal's length requirements.  However, some of the information (particularly the methods section) has citations.

Should these citations only be referenced in the supplementary information section or in the main part of the article as well?  And how would the numbering work for that?
Citations that do not appear in the main article should not appear in the bibliography section of the main article. Instead, you should create a separate references list in the supporting information, and use a separate numbering scheme. Usually you can use the same numbering scheme as in the main article; it will be clear that references apply to the supporting information, rather than the main article. (You could add a footnote to that effect if you want to make this clear, since supporting information is usually handled "as is" by the publisher.)