I think the first thing to decide is what you want. Is the goal to cover the distance quickly or do you want to take plenty of time for sightseeing and relaxing? Related to this, do you want to plan as much as possible ahead of the trip or do you want to be flexible and adjust plans on the fly? Flexibility is great as you can adjust your trip depending on how things go (wind, rain, break downs, spending more/less time at places, unexpected things to see, etc) but as it's high season last minute accommodation may be hard to find in some areas (in my experience rarely a big issue) and, specially if you're picky with your accommodation, may be more expensive and cheaper options may be sold out.
For example, how to most efficiently split the route into smaller sections,
Largely depends on your personal preferences and priorities. On my first bike trips it was mostly about biking and just rode and late afternoon I started looking for a place to sleep. Over time I moved away from cycling for cycling and now see it more as a good mode of transport. The consequence is that stages are more decided around what there is to do/see. If the distance between two sights is too far for a days ride I look for a place that might offer a decent off the beaten track break or just see how far I get and near days end start looking for a place to sleep.
how to find accommodation (i signep up on warmshowers, does this work?),
Nowadays there are plenty of apps that offer a fairly comprehensive 'real time' view of what is available. There are some apps for campings too, but in my experience they lack the comprehensiveness of hotel sites. If you have camping gear with you it's also possible to simple find a decent quiet spot to put out your tent, I think however that this is mostly illegal (but often tolerated) in Germany and plain illegal in the Netherlands so if you go that way keep a low profile and camp out of sight. No experience with warm showers, couchsurfing etc. in general non-professional accommodation is harder to arrange last minute.
which app to use to navigate and so on.
Personally use a dedicated gps with maps.me as a backup on my phone. There are plenty of apps out there, I don't know which ones are best. I guess it depends on personal preferences. I would in general advice to use an openstreetmap (osm) based app that supports offline maps. Specially for Netherlands and Germany osm is of very high quality.