Those flashbacks with ciri happen on their own during the main story, no need to worry about missing them. When characters like the baron or dandelion tell geralt about seeing ciri, you'll automatically jump into playing as her for a bit through important story beats. Pretty cool way they handle it actually, since you experience her path directly through quests like family matters instead of just hearing about it. The segments are short but give you all the important bits about what she's been up to, and they flow right into the regular story without any fuss. Just keep following the main quests, and you'll see everything important from her perspective when the time comes naturally.

Good to know you'll get to swap over to controlling ciri during these parts which is actually really fun to play through especially since her abilities are quite different from geralt's stuff. Just focus on the main story path, and the rest takes care of itself no problem.