Wow, I only read the first two paragraphs and am suprised to hear how much it sounds like Sikhism!
Amardeep; perhaps this analogy will help you.
We know that there are three parts to an atom, the electron, proton, and neutron. Then there are subatomic particles that make up each atom, like the quark. It will be awile till science discovers the next step; personally i dont think they will ever find the end to guru's Creation. But anyway, think of God/guru/Spirit/soul whatever you want to call it, as, say another subatomic particle, or something proven but intangible; the magnetic poles, love, time, the sikhtron (yes i know thats not a documented term, i just made it up for the sak of the example). Its hard to get your head around when you been brought up on something else your entire life; I still dont understand it to the point of Oh! or whatever, but i understand the principle of it.
Like when you're in second grade or so, and the teacher is trying to explain the concept of time. How to get that first understanding? That is the most difficult.
Reference:: Sikh Philosophy Network http://www.sikhphilosophy.net/sikh-sikhi-sikhism/8536-who-is-god-in-sikhism.html
When you think of say, your keyboard, and its shadow. You think they are entirly different things, but we know there is a reason for these. Dont think of the wind as air, it is God. Why does the wind blow? Because of the wind over there? Humans breathing? God is in the buttons you press, the lungs you use to breathe air into your body, the greass outside. "just because you can't see it doesn't mean it isnt there."
Reference:: Sikh Philosophy Network http://www.sikhphilosophy.net/showthread.php?t=8536
Clear as mud? Hope i made some sense. :P
Sat Sri Akal