We can voluntarily try to be grateful by acknowledging the good things happening during a bad phase. But, how do we whole heartedly accept it and do this subconsciously?

Writing down what you are grateful for helps put things into perspective. When we see something, we process it faster. So writing it down allows us to notice what we have during a tough situation.

I will do my best to answer this question. Before I answer this question, just want to highlight the fact that it sounds as though whoever wrote it was trying to highlight finding the good in the bad. This to me seems to highlight a huge problem in our current way of thinking about mental health. There's a huge emphasis on changing our thoughts, flip them from the negative to the positive. I think that there are two different things here at play. On the one hand there is reminding yourself to be grateful for the things that you are actually already grateful for, but due to reasons of depression and anxiety your vision is clouded, and due to this fact you don't see the things to be grateful for.

See the gorilla experiment with the basketball.

Secondly you have acceptance, which is different from gratitude. In a bad situation acceptance is really referring to not attempting to remove painful thoughts. So instead of removing painful thoughts with thoughts of gratitude, you are accepting of the painful thoughts and converting your emotional response into resilience, fortitude, growth, and ultimately to live a life which is aligned with your life meaning or your core values.

You might also in some instances be grateful for the opportunity for growth or the lessons learnt but this is definitely not to be confused with accepting painful emotions, and expanding your ability to contain them an act effectively in the world.

Hope this answers your question.