I want to send ibeacon and eddystone packets simultaneously from one beacon(PiBeacon). Actually, I'm running different commands in 2 terminals, each one for one of those protocols with an interval time, it works and it sounds good, but I just want to know if there is a smarter way to do that?
Using a time interval to switch back and forth between two beacon transmissions is a pretty standard approach called "interleaving". It is often used on both embedded hardware beacon transmitters as well as software beacons like the PiBeacon. When using a single Bluetooth chip that supports only a single advertisements, this is the best approach available.
Bottom line: You are doing the right thing.