In the case of 2 LEDs it is probably ok. You could consider just electrically joining them if they are supposed to be identical, but software is probably easier.
In the more general case where you may want to do lots of LEDs and these could be at different times and out of phase, then you need to keep the data and the code separated so that each LED has its own context (eg, pin, timer, status, etc). The data is then passed to the code (in this case as a parameter to the function, maybe) implementing the Finite State Machine (FSM) to run the FSM on the data supplied. This is the essence of what MultiBlink2 does and Beacon is very similar.
If you are new to programming it is worth studying these pieces of code as they are the key to how you do things on the Arduino (or any single tasking computer) without holding anything else up. Maybe start by reading about FSM and then look at how they are implemented in this code - Beacon is a lot simpler than MultiBlink.