What you need to do is design the operating system. Even if, for example, you decide it should be a UNIX-like system, there are still lots of decisions to make. How much like UNIX do you want it to be? Which parts of UNIX do you like and which do you think need improvement?
If you aren't set on its being UNIX-like, you end up with even more questions to answer: should processes form a tree, or are they "flat"? What kinds of inter-process communication do you want to support? Do you want it to be multi-user, or just multi-tasking (or possibly single-tasking)? Do you want it to be a real-time system? What degree of isolation do you want to provide between tasks? Where do you want it to fall on the monolithic vs. micro-kernel scale? To what degree (if any) do you want it to support distributed operation?
I'd generally advise against studying the Linux kernel for your inspiration. That's nothing against the Linux kernel itself, but a simple fact that Linux is intended primarily for production use, not education. It has lots of optimization, backward compatibility hacks, etc., that are extremely useful for production but more likely to distract than educate.
If you can find it, a copy of Lion's book (Lions' Commentary on UNIX 6th Edition, with Source Code, by John Lions is a much easier starting point. 6th Edition UNIX was still small and simple enough to read and understand fairly quickly, without being an oversimplified toy system.
If you're planning to target the x86 (at least primarily) you might also want to look at MMURTL V 1.0 by Richard Burgess. This presents a system for the x86 that uses the x86 hardware much more as the CPU designers originally intended -- something most real systems eschew in favor of portability to other CPUs. As you might guess, this tends to be oriented much more heavily toward the hardware end of things. Doing a bit of looking, however, this is apparently rather hard to find any more -- used copies on Amazon show up around $200/copy!
Fortunately, there are quite a few more possibilities as well -- Operating System Design and Implementation, by Andrew Tanenbaum and Albert Woodhull, for example.