Doubts and Meditation
You can practice the 4 Foundations of Mindfulness:


  These, bhikshus, are the four focusses of mindfulness that are to be cultivated for the abandoning
  of these five mental hindrances.


(Satipaṭṭhāna) Nīvaraṇa Sutta

Also,


  one understands and sees, as it really is, one’s own benefit,
  
  one understands and sees, as it really is, others’ benefit,
  
  one understands and sees, as it really is, the benefit of both


(Nīvaraṇa) Saṅgārava Sutta

One also can try developing the 7 Enlightenment Factors to overcome it. See: Āvaraṇa Nīvaraṇa Sutta

Wise attention can be used to overcome dought:


  Bhikshus, no other single thing do I see, on account of which unarisen doubt does not arise,
  and arisen doubt is abandoned, as on account of this, bhikshus, namely, wise attention.
  
  Bhikshus, through wise attention, unarisen doubt does not arise, and arisen doubt is abandoned.


Nīvarana,pahana Vagga

Also, do not feed dought. See: (Nīvaraṇa Bojjhaṅga) Ahara Sutta

Also see: Nivarana and Vicikiccha by Piya Tan