The author of Bilvavi Mishkan Evneh, in Vol. 5, in Ma'amar 10 in the section called "Pirkei Avodah U'Machshava" brings down a fundamental dispute about whether simply doing the physical mitzvos is the main thing or whether the kavannah, the intent and thought one has while performing during the mitzvah is the main thing. In that context he says (paraphrasing):
One must first understand that one can call both the basic physical act of doing a mitzvah as well as the intent, the "main thing." Let's explain. And through this explanation, we can understand the Nefesh Hachaim's statement that the physical act of doing a mitzvah is the main thing.Click here to get Dixie Yid in your e-mail Inbox or here to subscribe in Google Reader.
If you give someone a cup of water, what is the "main thing?" Certainly it is the water. However, if you give someone water without a cup, it is worth nothing since the water will merely spill out. In short, if you give someone a cup without water, the "main thing" is missing. Nevertheless, it is possible to get some water from another place. It comes out that even though the "main thing" is the water, nevertheless, water without a cup is nothing, but if you give someone a cup without water, you have still given him at least something.
It is the same thing exactly with Mitzvos. "A mitzvah without intent is like a body without a soul." This statement is not a mere aphorism. Rather, it is a very deep statement. The act of the mitzvah is the vessel and the intent is the light, the water. Therefore, a mitzva's intent alone is nothing because it has no vessel to contain it. But a vessel without light, a mitzvah without intent still can fulfill one's obligation because it is possible to fill up the vessel from elsewhere. (i.e. through others' mitzvos or through one's own mitzvah on another occasion) V'dai l'maivin. This is a deep idea for which one needs a basic understanding of "chochmas ha'emes." Without a basic grasp of this field, one will have a difficult time understanding this. It will appear as mere philosophy, but the truth remains the truth.
It is important to point out here that a ben Torah can sit and judge whether physical mitzvos or intent are more important. He can bring proofs from sugyos in Shas this way and that. But there is a basic problem with his approach. There are certain topics that a person must understand that he doesn't have the required knowledge, the tools with which to judge. It's not enough to know the Gemara. One must have a fundamental understanding of things, and where each thing in the world is derived from Above. One without a correct knowledge of this is unable to affix an importance to anything. With halacha, it is understood that that which takes precedence is not necessarily more important... (like the din of "tadir v'she'eino tadir, tadir kodem" which speaks to sequential order, not to inherent importance).