checkpoint placement is less about level length and more about how frustrating it would be to die in a specific part of the level and have to re-do a lot of things. you kind of develop a feeling for it, the more levels you make. for the way i structure my levels, i usually end up with a checkpoint every 6 to 10 screens, but your mileage may vary. while designing, think about the last part you built: "would players want a break after this? is this part good as a first challenge after a checkpoint? does the gameplay change here significantly (new mechanic, autoscroller starts, autoscroller ends, boss, ...)?"
perceived level length is also less about actual level length and more about level content. your level is too long as soon if it starts to be boring. your level is short if players leave it wanting more (not necessarily a bad thing as shorter levels are more replayable!). this is hard to quantify as the designer, which is one of the reasons why having some people test your levels is crucial. you can also develop a bit of a feeling for this over time, but it's harder for me to put into words than in the checkpoint case.