Most programmers who write applications for X will use third party toolkits.
If you are interested in writing an application that uses X primitives directly without the use of a toolkit, you can use the Xlib interface, painful though it is.
The documentation for the Xlib interface can be found here:
O'Reilly & Associates have also made freely available online some of their classic X programming manuals. These are a bit older, dating from the X11R3, R4, or R5 eras, and the toolkit ones cover Xt-based toolkits which are no longer in widespread use for new applications, but much of the Xlib documentation still applies, it just doesn't cover all the new additions:
Xt & Xt-based toolkits: