I will start with some questions, then reference some scriptures that seem to me to address these questions.  Since my friends who comment here are mostly Christ Followers I will quote from the New Testament.

Is it a sin not to go to church on Sunday?  

During the period I attended a Protestant church, up to the age of thirteen, I remember being led to believe it was a sin not to go to church on Sunday.  My guess is that as long as you spend the Sabbath in worship of God it should not matter where you do it.

Does it manner in which you worship God make any difference?  

My perceptions is that worshiping God means making sacrifices in his name and following his guidance. 

I can understand that following the traditional method of worship service for the church you belong to reinforces your bond to their doctrine/ guidance.  My guess is that to your God the only thing that counts is the degree of faith to him you demonstrate in your worship service. 

From the Bible (King James Version)

Mathew 18:19-20

19Again I say unto you, That if two of you shall agree on earth as touching any thing that they shall ask, it shall be done for them of my Father which is in heaven.

 20For where two or three are gathered together in my name, there am I in the midst of them.

Acts 2:1

1And when the day of Pentecost was fully come, they were all with one accord in one place.

Acts 17:24

 24God that made the world and all things therein, seeing that he is Lord of heaven and earth, dwelleth not in temples made with hands;

1 Corinthians 14:15

15What is it then? I will pray with the spirit, and I will pray with the understanding also: I will sing with the spirit, and I will sing with the understanding also.

Hebrews 10:25

25Not forsaking the assembling of ourselves together, as the manner of some is; but exhorting one another: and so much the more, as ye see the day approaching.

1 Peter 2-5

5Ye also, as lively stones, are built up a spiritual house, an holy priesthood, to offer up spiritual sacrifices, acceptable to God by Jesus Christ.