I think PoundlsPoundan0 is right with regards to loading in files, hard coding stuff into your game is not good practice, also, using external files allows you to add more in the future etc.
With regards to how to store this information it totally depends on what kind of shoot em up you're talking.
If it's a scrolling game then you want to store the x,y of each of the enemies and then spawn them when they're about to come onto the screen.
If it's a space invaders type game where you're spawning things to appear then you could use a counter variable as the level progresses.
Either way, external files are the way to go for future scalability and flexibility.
With regards to how to store this information it totally depends on what kind of shoot em up you're talking.
If it's a scrolling game then you want to store the x,y of each of the enemies and then spawn them when they're about to come onto the screen.
If it's a space invaders type game where you're spawning things to appear then you could use a counter variable as the level progresses.
Either way, external files are the way to go for future scalability and flexibility.