In this poem, Tagore compares reason in its ideal, perfect state to "a clear stream." In its imperfect state—improperly directed—reason is, Tagore implies, comparable to "a dreary desert sand of dead habit."
A clear stream connotes clarity, movement, and direction. The implication is that reason, in its ideal state, should be clear rather than muddled, lively rather than still, and directed or purposeful rather than purposeless. A stream also eventually "becomes" or feeds a river, which, in turn, eventually becomes or feeds an ocean. Thus the comparison implies that reason purposefully directed will eventually become or feed something bigger than itself, whether that be a bigger thought or a practical application of the initial thought.
On the other hand, a desert is a barren environment, lifeless and still. A desert is a hostile environment for life just as a mind that is lifeless and still is a hostile environment for thought. A desert, unlike a stream, also does not obviously become anything bigger than itself.
In response to your second question, I think the poem implies that our actions are governed by both the clear, purposeful reasoning symbolized by the stream and by the still, lifeless reasoning symbolized by the desert. One might infer that the better actions are governed by the first type of reasoning.