Please remember; not is an adverb and to is a preposition. To should either be followed by a verb to form infinitive or a noun or noun phrase but not an adverb such as not. So your first sentence should be:
He told me not to waste my time with you.
Placement of an adverb in sentence is very important in order to avoid ambiguity. It is a common practice to place the adverb after the auxiliary but before other verbs. So your second sentence should be changed to:
They have not decided to repair the car (formal)
They have decided not to repair the car.( informal)
not to say is a common phrase used when adding a stronger description of something in stead of the phrase not only ... but also:
The information is inadequate, not to say misleading.
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