You have a couple of questions here.
Yes you can use the LETIMER (which is what I think you mean when you say LERTC) peripheral independently of the RTC. They are separate peripherals, but note that the LETIMER is clocked from the same clock as the RTC.
As for using the external crystal oscillators, you need only enable the clocking sources that you actually use. However, clocking sources and entry/exit of the various low power energy modes interact. It can be rather tricky and complex. I suggest you use emlib to control these peripherals and in particular to enter and exit lower power energy modes.
If power consumption is important to you, note that high frequency clocking of the processor core consumes lots of power. Of course this must be traded off with how long you remain awake before going back to a lower power mode and with any real time requirements you might have for processing. Pushing off work to peripherals and using DMA to perform data movement is generally a win. Expect to do a good bit of tuning and you will need ways to accurately measure the power consumption. Using internal RC oscillators for clocking may be sufficient and a lower power approach. The low frequency external crystals tend to be 32 KHz clock crystals and don't consume that much power. They are a good alternative to the internal RC oscillators if you need better frequency stability.
