According to the eNotes guide on the work, it is "a didactic poem, a work meant to give instruction. In this case, “If” serves as an instruction in several specific traits of a good leader." So consider each stanza to be a specialized set of advice for a young man trying to become great. Your question about the "waiting and dealing in lies" relates to the first stanza, so let's take a look at that specifically (available at poemhunter.com):
If you can keep your head when all about you
Are losing theirs and blaming it on you;
If you can trust yourself when all men doubt you,
But make allowance for their doubting too:
If you can wait and not be tired by waiting,
Or, being lied about, don't deal in lies,
Or being hated don't give way to hating,
And yet don't look too good, nor talk too wise;
When Kipling refers to "waiting," he isn't neccessarily talking about waiting for something specific, but rather the art of waiting in general. In other words, he's reinforcing the virtue of patience. He tells his pupil that if he can be patient with other people, with himself, and with waiting for things to happen, he will show himself to be a leader. This must be true patience, without resentment, for Kipling explicitly says that not only must the pupil "wait," but also "not be tired by waiting" (5).
Kipling also speaks to lies and how to deal with them from both sides: receiving and creating. First, he cautions the pupil to not be "tired" by "being lied about" (6). Kipling is pointing out that sometimes, and especially on the road to prominence, people will lie about others, whether it's for their own gain, out of spite, or to disadvantage or humiliate another person. A leader must not be tired by this--in other words, he must accept that it will happen and give it no importance. Kipling also makes sure to remind his pupil also to not "deal in lies" (6). So not only must the pupil not put importance on lies about himself, but he must also consciously resist using lies about others as currency in his climb to success. He shouldn't create them, believe them, or spread them.
Kipling invites his pupil to rise above the common, base instincts of the average human being striving to compete in this world through shady means. He wants this "son" to become a leader the hard, but honorable way, accepting that others will fall short of his example and always striving to set the good example. As the eNotes summary puts it, this stanza "provide(s) instruction in the maintenance of righteous behavior in the face of unrighteousness."