You can theoretically layer all 64 sprites on top of each other if you had wanted it, but always remember the PPU can't show more than 8 sprites per scanline. Sometimes you can get away with layering sprites but in most cases (in action oriented games), it tends to become impractical really quick.
When layering sprites over BG, you typically want to avoid doing it in the "active" field of play, that is, anywhere where a lot of sprite-based entities will be on the same y axis a lot. For example a moon in the sky in a platformer or the like is a good use of this technique.
For static screens, it's free for all as long as you respect the basic limitations. Here's an example i did a while ago
where sprites are used to mask attribute clashes and add a bit of highlight here and there as well. It using almost every sprite in 8x16 mode, so there's not much wiggle room left. Here, you can see the difference when the sprites are disabled
To answer the question, i don't think NESmaker needs to support a special case. just place an entity on top of another and you have sprite-on-sprite layering. Or just place an entity somewhere withot movement and you have a static sprite on bg layer. It just needs to be applied very moderately in order to not cause trouble in other ends. NES game design is all about balancing between pitfalls, even with a nifty tool like NESmaker.