They are okay. A relay is just passing current. One of the circuits will be the coil to operate the relay contacts and the other will just direct the flow to whatever is being powered. The coil doesn't care about polarity. If you look at the wiring diagram on the relay you will see which contacts go to which circuit. Then look at the end of the relay with the terminals. They will be numbered. Notice that contacts for each circuit are diagonal from each other. No matter which way the relay is inserted into the fuse box, the circuits will be powered correctly. Obviously none of the above applies to five pin relays. 
