Deep or Med Box for Nuc & Package question

My wife and I have just hived our first hive from a nuc ,we ordered 1 Nuc and 1 Package.I was told to start with all med, so that is what we ordered ,I found out after I ordered our supplies that the Nuc would be coming on Deep frames then so I ordered deep box and frames and all is good , my question is, do I always leave the deep box and just change out frames in the bottom box or can and use med on top or can I use med frames in deep box? I plan on using a med box with the pacake when it arrives.I hope this makes sense... this is our first time as beekeepers and love it.