He explains that in Tefillah two things are supposed to happen simultaneously. Our eyes should be focused downwards while our hearts should be in the heavens.
I find this particularly challenging at least in a semi-literal sense, but lets try and understand what he's saying a little more. He actually goes into more detail and explains that the focus of our eyes should be on the low things to truly understand and internalize that HaShem imbues everything no matter how small and seemingly insignificant. Whereas our hearts should be in the heavens means above the seven middoth, the seven attributes, which represent the seven days of creation, all the way back to HaShem's Hochmah, His Wisdom that precedes everything.
We find when we look at it properly that, at least as it seems to me, the Rebbe is telling us that we have to unite everything back to its source. Meaning more simply, with our hearts we need to know that HaShem's Wisdom intimately pervades and plans everything in existence, while with our eyes we need to seek out the actual presence of HaShem's wisdom in even the lowest levels. In this way we become a ladder whose feet (and eyes) are firmly on the ground, but whose head (and heart) reach to the highest places in heaven.
It seems to me that this connection takes advantage of something Chazal tell us about the connection between the eyes and the heart, namely the eyes see and the heart desires. When we see something (desirable) with our eyes, it arouses a great desire for that object in our hearts. Here we make use of this by first seeking out HaShem's highest Wisdom in the lowest of places, those closest and most easily accessible to us, and once we begin to see this Wisdom, our hearts greatly desire it and run to the heights of heaven to acquire it. Perhaps this is why the Rebbe first mentions "lower your eyes", and only then, "and raise your heart to the heavens."