Ordering information about computer science

I'm a computer science student. For the last several years I've gained a good knowledge of programming, mostly Java/PHP/C++ and general principles of object-oriented programming and structural programming, some information about databases, operating systems and networking. I've been studying electronics for a couple of months and I'm getting better at it.

However, I still have problems with combining all of that stuff that I've learned about to develop complex applications, for instance when I try to write an application that uses networking and databases, I sometimes struggle with understanding how it's gonna work at a hardware level.
I literally struggle with putting all that knowledge about physics, math hardware, programming, networking, electronics into practice. A good engineer should have that ability to combine various disciplines to develop something, is he? ;-)

Hence I'm looking for some ideas how to organize and combine all the knowledge I've gotten so far so that I could understand what's going on at particular levels for instance hardware, networking or compilers?

Is it a good idea to start developing applications that use multiple levels of software including electronics, hardware, databases, networking etc?

computer science students basically knows oly about how to programming.but while comparing to hardware level its difficult to understand the basic operaction of the hardware...try to know the basics of hardware and develop a application with the functionality of hard ware.If you are good in C or C++ try embedded c which is nothing but c-programming to perform some specific operactions in micro controller or in microprocessor...

All the best

try to learn c for hardware programming.