It doesnt stop you from understanding it, but there can be tar pits in some areas.
I RE embedded systems everyday and I pretty much use a handful of things:
Primaries: IDA PRO and GDB
aside from that I use a hand few of custom tools and a lot of python.
There really isnt any book I can give you, and there really isnt an order. First I would read the book "Real time concepts for embedded systems" Then I'd read the book for the microprocessor the device runs on.
Aside from that it just takes a lot of doing and a good support team. There is not much info out there on REing embedded systems so having people to goto for questions is essential.
Keep in mind though, RE work is resource intensive. A single person with 5 years of experience, who works on a small device can take between 3-12 months to RE the device depending on the objectives.