All the info you need is in the chip datasheets with those simple 8-bit MCUs. Both Microchip and Atmel supply very complete and easy to understand (imo, I guess) documentation, go there first. I found the MSP430 docs to be slightly less accessible due to them being split up into several documents, but they're certainly complete as well.
You can use the Arduino IDE to ease into things if you like, by not using the supplied libraries but starting to work with the processor registers directly. It's probably not a good idea to mix and match library calls and direct register access, because those lib calls are doing quite a bit more than you'd think. If you want to start with a proper IDE, yeah, you'll likely have to do a good part of the setup yourself, but it's not that complex with 8-bit MCUs. Something like the SPI hardware controller will have between 2 and 5 registers with options you can set, such as baud rate, bit order and polarity, and if the defaults happen to work for you, maybe all you need to do is set the "enable" bit.
With the Arduino IDE, you also get the source code. Go have a look at the source for the digitalWrite() function for example. Reference that to the datasheet, and you should get a pretty good understanding of how the chip works. And, probably, some distaste for Arduino, as you realize how much performance they sacrifice in their effort to tolerate coding errors.