You have these issues at every scale of the electronics design process, even in PCB layouts. With a lot of experience, you’ll become better at gauging what works, what doesn’t, and what issues might arise. Certainly simulation is part of it, but you have to be able to start from a large knowledge base and be able to adapt some existing circuits to suit your needs.
There are a lot of general design rules, like keeping digital clock sources away from analog signals; separating digital, analog, and power grounds as well separating power supplies are usually a must. Differential signal pairs have to be routed together, which helps them cancel noise. Ground planes have to be stitched to avoid any islands. Sharp corners are a no-no for fab and current density reasons. Temperature sensitive circuits have to be kept away from power supplies. If you run out of options, you can move things to different layers, but that may be more expensive or not an option for your process.
Experimenting on silicon is more expensive than PCB, but there are ways to put some test parts on a shared wafer with other projects. There are maskless prototyping tools, but the features are pretty large. Source: designed and built some of said tools.
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