importance of flowchart!

Flow charts are a graphical representation of code, Program states or even SRAM contents, if used in a creative way. Once you know how to use them for code you'll quickly develop your own style to create flow charts for almost anything.
When you think about implementing a special algorithm or peripheral driver it might be better to have a flow chart already done before you start hacking code. And trust me, that will save lot of time. If you have code that is not sufficiently commented or just BIG, analyse it by making up a flow chart. Very often that helps, especially when you got it from the web.
Especially when writing code in assembler they are a great help, because assembler instructions are not always self-explanatory and even well-structured code will get hard to read once it has grown to a certain size.

You can find a good program for editing flow charts at www.rff.com. But a piece of paper will do the job too if you need to make up one.

lets start from the scratch

I found the blog very nerdy..and not at all helpful for people who have to learn from the scratch. So, I think this post will be a little more helpful.
ok...so the basic question...
What is a Microcontroller?
Microcontroller can be termed as a single on chip computer which includes number of peripherals like RAM, EEPROM, Timers etc required to perform some predefined task.
But, it is not a computer!
Wikipedia provides further details about AVRs.
we are talking about ATMEGA 16...
 

Also, Architecture can be seen in the datasheet.
Now coming to the programming part, the ASSEMBLER. Here is a link for it.
I hope this helps. This post will be further updated.
For PCB designing please follow this link . It is very helpful.