I have loaded some Agilent data, and normalized it such that I now have an EList object.  The expression values are in elist$E and the probes in elist$genes, but elist$E does not have any row.names.  Can I assume the expression values in elist$E and the probes in elist$genes are in the same order then so I know which expression value goes with which probe?

By default read.maimages() reads in the gene info into the 'genes' list item, and (unless you made changes directly to the elist$genes or elist$E list items), they will be in the correct order.

When you fit a model and make comparisons, and ultimately use topTable(), the gene info from the genes list item will be used to annotate your results.