Channel A for 100MHz, Channel B for 1090MHz, at same time,is that OK?

Short answer: you can’t

RX @ 100MHz and RX @ 1090MHz at the same time using one LimeSDR USB/PCI device is not possible. Because both RX channels share a common fractional-N PLL synthesised LO. The frequency difference between two similtanious RX channels is limited to being within the same 61.44 MHz of bandwidth. Even though there is a seprate analogue path for both RX signals you could still look at the extraction of the two RX channels as happening in the digital domain. Conceptually it might make it easier to understand.

But you can RX at any frequency within the devices operational range and similtaniously TX at any frequency within the devices operational range (because there is a seperate, but still sharing a common clock, fractional-N PLL synthesised LO for TX).

EDIt: I’ll also point you at the Functional block diagram: LimeMicro:LMS7002M Datasheet - Myriad-RF Wiki