Were are srecet pass ways and places?

If by seret passageways the asker means flashing arrows:EVERYWHERE, and each one leads to somewhere different. If the askert means literal 'secret' passage ways, then there are none. There are a few arrows that take a while to find, or lead to another fairys 'home', but otherwise, thre are no secret passageways.

When discussing "secret" passageways, I believe you're talking about the ones inaccessible by a simple arrow, or "treasure areas." There are four, if we're not considering the gem-mining minigame with Iridessa (cave), one for each season:
Spring: there's a flower that is visible by the cherry blossom tree. Click on the arrow above it to enter it's grotto, then draw a triangle 3 times over the flower. It'll open and an orange sparkle will appear, which is the mark of the treasure areas.
Summer: Every full moon in the area with the Minister of Summer there is an orange sparkle in the water.
Autumn: Entering the fall area, click the right arrow, then the one into the log. There will be a patch of mushrooms. Draw a triangle 3 times over the right-most mushroom and it'll tip over to reveal an orange sparkle.
Winter: Entering the winter area, you need to be quiet as you sneak to the rainbow butterfly resting. Tapping on it when you're in range will cause you to spin around it and gently wake it up. The butterfly will be happy, fly away, and reveal the orange sparkle for you to tap on.
Inside these treasure areas, you have a chance to collect 15 items related to the area, then remaining time used for the rainbow bubble with a rare item (usually clothing), or 20 fairy medals each worth around 20 fairy medals, then the remaining time used for the rainbow bubble with around 400 fairy medals.
I hope this helps! :-)