How to use inner feeling (intuitive feeling) while taking refuge
Taking refuge in the Three Jewels means to make effort to receive the blessings of Buddha, making effort to put Dharma into practice in our daily life and making effort to receive help from our Sangha community and in particular our teachers. 
Blessings are anything that transforms our mind from negative to positive, that increase  our faith etc. A great way to do this is to remember that we are always in the presence of living, loving Buddha. 
There are a myriad of ways to put Dharma into practice such as simply being mindful of a verse of the teachings that has touched our hearts, developing equanimity and love, practicing patience, giving etc. 
Taking positive advice and encouragement from our Dharma brothers and sisters and considering advice from our teacher helps with the last one. Also, seeking to clarify confusion by discussing and debating are good too.