I'm not an expert, but I think English "that" has two different meanings:

1. this - that => это/этот/эта - то/тот/та
2. which => что

When you say something like: "I want to tell you that I like you", that essentially means:

I want to say a phrase, which would convey the meaning: "I like you". => Я хочу тебе сказать, что ты мне нравишься.

Alternatively, you could say: "I've been waiting to tell you that for a long time." => Я уже давно хотел тебе об этом сказать.

So, when you say something like: "Я давно хочу сказать тебе то, что ты уже сам знаешь." that would be a colloquial way of a better equivalent: "Я давно хотел сказать тебе о том, о чём ты уже сам знаешь." and that would mean: "I've been waiting for long to tell you something that you already know."

Hope it helps.