Yup, that is the nature with home theater processors and home theater receivers. I have used many different HT processors and the Krell On Screen menu configuration is actually not that bad. I have found the Krell menu system pretty usable once you understand the basics of what is required for HT processor configuration. That being said, every processor has slightly different behavior and configurability. I have recently worked with both an older low end Yamaha receiver as well as a new top-end Yamaha receiver. Both were configured in significantly different ways and, for some items, were much more complicated and confusing than the Krell Showcase configuration.
Krell has a single main configuration for the speakers which are shared across all inputs. The configuration of the speakers uses the first 3 items of the main menu:
CONFIGURE SPEAKERS - this allows you to select what kind of speakers you have (maybe you don't have surrounds or lack a center channel speaker). It also allows you to configure whether or not you want to crossover the speaker to have bass sent to the subwoofer.
LISTENING ROOM SETUP - this allows you to set the distance of each speaker to the listening position.
CALIBRATE VOLUME - this allows you to set the individual level of each speaker so that they are configured to be equal output. I always use "MANUAL NOISE SEQUENCE" so that the Krell outputs a pink noise sound test for each speaker. The idea is to adjust each speaker so that it outputs the same volume from the test signal.
Once you have configured the speakers, the next step is to configure any input devices you have using the "CONFIGURE DEVICES" from the main menu. Essentially, this allows you to define what happens when you click on an input button on the remote (such as DVD / LD / SAT / etc.). For example, you can configure the Krell to select the Component 1 video input and the COAX 3 digital audio input when you hit "DVD" on the remote. When configuring the audio inputs that use digital audio, you can also define the default mode when receiving a particular type of signal. For example, when Krell receives a PCM signal, you can configure to use either STEREO or Dolby Pro Logic. This can always be changed. It is common just to leave the configuration as is on this setting, so I wouldn't worry too much about it.
The last main menu item "CONFIGURE LEVELS" gets into some advanced configuration that sometimes isn't common. I wouldn't worry too much about these setting. The Krell will operate just fine using factory defaults, but you can read about these configurations in the Krell documentation.
Hope this helps.