how do i make it rain?

I hope you already have rain tiles. If you do, make a screen off to the side (or on an entirely new map) completely full of rain combos. On the screen(s) you want rain, go Data -> Layers. (In ZC 2.5, the Data menu is known as the Screen menu.) You should first learn this basic chart about layers:

<Highest>
Layer 6
Layer 5
Flying enemies
Layer 4
Layer 3
All other enemies and Link
Layer 2
Layer 1
Combos on the main screen (this is often called "layer 0"😉
<Lowest>

In other words, layers 1 and 2 are under all enemies and Link, but will appear over top your main screen's combos. Layers 3-6 will cover up Link and all enemies. Layers 5 and 6 will cover up not only those, but also flying enemies. In this case, you want the rain to be on layer 6 (the "highest" possible). In the layer 6 column, designate the map/screen your rain is on. Simple as that.

Also, note that transparent colors will not appear on layers (hence the term "transparent"😉. This is important to utilize.