The IDE does saves you the trouble of having to run them all independently, but doesn't really hide them: the IDE still needs you to configure each of the tools, and the Build Progress window shows each one running in its turn.

As Ashish says, it is still important to understand the roles of the individual tools; eg, the difference between whether an error is a Linker error or a Compiler error makes a big difference to how you approach fixing it...
eg, see this thread, where some code copliled fine, but wouldn't then link:
http://www.8052.com/forum/read.phtml?id=85489
(Note that the poster incorrectly attributes the Linker message to the Compiler!)