Here is an extract from MN 19, that I feel provides good guidance on the separation of wholesome and unwholesome thoughts.
I apply it in my practice and can vouch for its benefits. So can the Buddha!
MN 19: Dvedhavitakka Sutta
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The Blessed One said, "Monks, before my self-awakening, when I was still just an unawakened Bodhisatta, the thought occurred to me: 'Why don't I keep dividing my thinking into two sorts?' So I made thinking imbued with sensuality, thinking imbued with ill will, & thinking imbued with harmfulness one sort, and thinking imbued with renunciation, thinking imbued with non-ill will, & thinking imbued with harmlessness another sort.
"And as I remained thus heedful, ardent, & resolute, thinking imbued with sensuality arose in me. I discerned that 'Thinking imbued with sensuality has arisen in me; and that leads to my own affliction or to the affliction of others or to the affliction of both. It obstructs discernment, promotes vexation, & does not lead to Unbinding.'
"As I noticed that it leads to my own affliction, it subsided. As I noticed that it leads to the affliction of others... to the affliction of both... it obstructs discernment, promotes vexation, & does not lead to Unbinding, it subsided. Whenever thinking imbued with sensuality had arisen, I simply abandoned it, destroyed it, dispelled it, wiped it out of existence.
"And as I remained thus heedful, ardent, & resolute, thinking imbued with ill will arose in me. I discerned that 'Thinking imbued with ill will has arisen in me; and that leads to my own affliction or to the affliction of others or to the affliction of both. It obstructs discernment, promotes vexation, & does not lead to Unbinding.'
"As I noticed that it leads to my own affliction, it subsided. As I noticed that it leads to the affliction of others... to the affliction of both... it obstructs discernment, promotes vexation, & does not lead to Unbinding, it subsided. Whenever thinking imbued with ill will had arisen, I simply abandoned it, destroyed it, dispelled it, wiped it out of existence."
Whatever a monk keeps pursuing with his thinking & pondering, that becomes the inclination of his awareness. If a monk keeps pursuing thinking imbued with sensuality, abandoning thinking imbued with renunciation, his mind is bent by that thinking imbued with sensuality. If a monk keeps pursuing thinking imbued with ill will, abandoning thinking imbued with non-ill will, his mind is bent by that thinking imbued with ill will. If a monk keeps pursuing thinking imbued with harmfulness, abandoning thinking imbued with harmlessness, his mind is bent by that thinking imbued with harmfulness.
Metta,
Retro.