As it is a small company, draft a standard set of questions targeting the output you want - not everything... and interview each one within a 20 minute time frame. This targeted and brief approach will ensure they give you their real concerns, versus having time to create what they think you want to hear. I do this often with my clients as I tell them 'truth sits on the surface'.. what comes up for someone first, is their truth, so don't exaggerate the time. Keep it short and sweet.
I would recommend carrying out a survey as a starting point, then running a focus group to probe further on the results from the survey. You could also meet with them all individually and ask the same structured questions of them all. In order to maintain confidentiality they could be numbered one to six. I hope this helps.