Spiritual Path

I seek enlightenment. My understanding is that aneros will help me with this by activating my lower chakras.

That's great that you are seeking enlightenment but thinking that Aneros use will activate your our chakras may be foolish. The whole concept of chakras, energy channels/meridians, kunadlini energy, etc. is in the realm of meta-physics and personal belief systems. As such it is almost entirely a mental construct not dependent on physical material such as the Aneros to achieve. IMHO, enlightenment is bestowed from within yourself when you have reached a certain level of equanimity and peace within yourself. There may be numerous paths to achieve that optimal mental state with meditation often cited as one such path. I have often referred to my Anerosessions as 'erotic meditations' but that is more a result of my intent to pursue pleasure than an attempt to reach a meditative state, though reaching the meditative state facilitates the flow of pleasure.

How can I meditate while using a massager?

The same methodology you would use to meditate without an Aneros in situ should suffice. The only allowance you might need to make is for unimpeded movement of the massager in whatever body position you choose to meditate.

What positions should I use?

The choice is totally up to you. Just as in yoga practices, body positions which favor entry into the meditative state will probably vary from individual to individual. You'll just have to experiment to find one most comfortable for you.

My primary goal isn't physical pleasure, it is to be enlightened.

A worthy goal to be sure, just remember that it isn't the Aneros which will get you there it is your own mind that will. As @B Mayfield (one of the most veteran Aneros users) once said, these devices are like "tantric training wheels", i.e. they may help keep you upright on the path but they are not the cause of your progress. Your progress is totally due to your inner mental processes.
Good Vibes to You !