You may not change these frequencies per se, because they are needed for BLE protocol timing. You may however change their sources, which might be what you are asking for? Please have a look at this answer by my colleague, it is old, but the concepts still apply.
Furthermore, I would definitely suggest following the advice of @awneil to familiarize yourself with the product, SDK and tools using the "Getting started" guide. For example, since the SoftDevices implement the BLE stack for you, you will not need to implement anything of this protocol yourself - you will only need to familiarize yourself with the BLE concepts and theory to quickly be able to get a working application up and running.
