Taking one verse out of context and then comparing it to another verse taken out of context is always confusing. So lets put those verses in context and also use the correct Bible reference:
Exodus 20:4-5
4 Thou shalt not make unto thee any graven image, or any likeness of any thing that is in heaven above, or that is in the earth beneath, or that is in the water under the earth:
5 Thou shalt not bow down thyself to them, nor serve them: for I the LORD thy God am a jealous God, visiting the iniquity of the fathers upon the children unto the third and fourth generation of them that hate me; KJV
Now if you take the time to read all God's instructions for the construction of the tabernacle you will find the purpose of the mercy seat and the cherubim.
Exodus 25:21-22
21 And thou shalt put the mercy seat above upon the ark; and in the ark thou shalt put the testimony that I shall give thee.
22 And there I will meet with thee, and I will commune with thee from above the mercy seat, from between the two cherubims which are upon the ark of the testimony, of all things which I will give thee in commandment unto the children of Israel. KJV
No Israelite bowed down to or served the images of the chrubim. The ark was a piece of furniture that contained the tablet of the law and was where God spoke to Moses. Also we can discern the Holy of Holies was a model of God's throne based on God's instructions for the curtains:
Exodus 26:1
26:1 Moreover thou shalt make the tabernacle with ten curtains of fine twined linen, and blue, and purple, and scarlet: with cherubims of cunning work shalt thou make them. KJV
The tabernacle was decorated with many images of cherubim. Also there were other images found in the tabernacle as well as Solomon's temple. For instance the bronze sea was supported by 12 oxen.
1 Kings 7:44
44 And one sea, and twelve oxen under the sea; KJV