In the AdenoZAP system, you will need to excise from your shuttle plasmid a DNA fragment containing the left ITR, the packaging signal and your expression cassette. Two enzymes are available to cut on the ITR side: PacI and SwaI. Make sure that the enzyme you choose does not cut inside your expression cassette. Since both PacI and SwaI are rare-cutting restriction enzymes that recognize 8 bp-sequences, having both of them in your expression cassette should occur very rarely.
If neither PacI nor SwaI cuts inside your transgene, there is really no preference. Because the PacI site is immediately flanking the start of the adenovirus genome, the DNA ends generated by PacI resemble the most the ends obtained from deproteinised virion DNA and might therefore be more efficient in promoting virus replication. In practice however, no difference in the time needed to recover the virus after DNA transfection into 293 cells is observed between both settings. Virus plaques can appear as early as 4 days after transfecting PacI- or SwaI-digested DNA into 293 cells.
If one of the two enzymes cuts inside your transgene, use the other one.
If both SwaI and PacI cut you transgene, eliminate one of them by site-directed mutagenesis, or use another adenovirus construction method.