I am building few tourism sites...in php.
Flash in my sites is only presented in menus....

Now I want to make headers in flash...main reason is to have animations like this

http://www.croatours.hr

or like this

http://www.templatemonster.com/website-templates/7961.html

.Sea waves and clouds and nice animation over pics

Is there a flash software and tutorials for it that can help me?

Well I'm not sure what clouds you're talking about on that first link, but as for the waves, as far as I can tell, this is what they did:

(first off, for this you need to have a decent understanding of masks in flash)

but a layer over the picture with a box that has a gradient from white to transparent. The white side being toward the top of the page. This box should start where you want the wave to start and become transparent where the wave will disappear.
Now create another layer and make it a mask over the layer with the box.
Here's the part that's tricky. Most likely each wave you see is an individual symbol that moves from top to bottom across the box in the layer below until it disappears as the trasparency reaches zero.
Now each wave symbols appears to basically be made up of tiny pixels, (either individually or a few together to make small shapes) close together and those pixels need to move a little to complement the movement to shore, either make them whole thing shape morph to a slightly different position or the horrible tasks of individually making each shape/pixel a symbol that will move.

I'll try to recreate this and let you know what worked for me and email the file so you can understand my process a little better.