It certainly does no harm to be aware of  'speaking in your head, from the heart' while you are praying this prayer. I mean, that one prays silently, but is aware of one's real, physical heart (perhaps even become quiet enough to hear it as you pray).

Breathing this Prayer
The prayer begins, 'Lord Jesus Christ, son of the living God, 
have mercy on me, a sinner'. 
This is straight from the gospels. 

You can time it with your breathing. I've heard people recommend that one say 'Lord Jesus Christ, on the 'in' breath, hold the breath for 'son of the living God', breathe out for 'have mercy on me', and hold for 'a sinner'. 

This can be really calming. I recommend it in moments of stress, for at the same time one takes control of ones mind, and ones automatic physical functions. 

Deliberately Changing
At first you learn to change deliberately from one section of the prayer to another.
From 'on me, a sinner' to 'on us'.  (I heard it explained that one can't make a judgement about any one elses sinfulness, potential or actual, therefore the prayer rests simply on 'us'). Then on to 'on us, and all your world'. 

The Everchanging Pool of Quietness

In fact, especially when you are first using it, the prayer becomes like a pool of rings circling out from yourself into the world and then back again. 

This prayer seems to have been a great favourite with the Orthodox 'Staretzim', and there are many wonderful books to be read about it and its affects. I like it chiefly because one quickly feels wonderful when one has prayed it.

Once when I was ill, I remember sitting up knitting while I used this prayer this prayer. It became like a pool of peace. Somehow after one had practised it, whatever one laid eyes on became 'us', 'us, and all your world' or even, crestfallen, 'me, a sinner'.