Good work on not using auto settings - credit deserved there, especially since only having it for 2 months. Usually takes n00bies a year or so to get the courage to rotate that dial
Anyway, looking at the first photo I'm inclined to believe it was an overcast sky? If this is the case, then you never took the photo wrong. However, this can be fixed in post processing. Have you breached into the world of programs such as Aperture (for mac) or Lightroom (for pc)? If so, then here's what I would do in the situation,
1) shoot the photo in raw. Not Jpeg (I dunno if you have done this or not). Raw retains more information as opposed to an uncompressed jpeg. They are larger file sizes however, so HD space over a couple of years may become a concern. But the benefits outweigh the costs.
2) in post processing, bring your highlights down - this should bring some detail back into the sky.
For your second photo, were you shooting into the sun? Perhaps a polarizer would help. Or - once you get really comfortable, you could look into doing some HDR work for scenes like this.
Your third photo - I like. I don't really see anything wrong with it.
Anway, hope this helps, happy shooting!