I believe that if you enable iCloud in iBooks, that will sync them.
Settings->iBooks, Sync Bookmarks and Notes should enable it.
Then when you close the magazine on iPad 1, (tap, then tap the less than sign in the upper left to close the magazine) iPad 1 should put a bookmark where you were. Open on iPad 2 and it should open on the same page and you should see the bookmark as red in the upper right.
This assumes that both devices have iCloud access. If they don't, then the bookmarking can't transfer between them.