When restringing your guitar, replace only one string at a time. This keeps the tension on the neck as close as possible to what it should be. Removing all the strings at once and then keeping the neck void of strings (and tension), only to reapply pressure again, poses the risk of neck misalignment and those annoying intonation problems that go with it.
Also, try to replace the guitar strings with the same gauge, or strings of a gauge that are as close to the previous gauge as possible. Again, drastic changes can cause intonation problems.
Restringing tools can also make the process faster and easier.