If you do choose to use an altar (and I do personally believe they are an excellent focus of both magic and deity worship in the home) then how you use it and how it fits in with your path is up to you.
Some altars are used specifically as a point of worship and intended solely for deity worship. If this is the case you may want to pick out crystals that you use to honour your deities or objects associated with deities themselves (silver candles, oak leaves, statues...). You may want to be selective about what you choose to offer to your Gods in which case your more valued items might take pride of place of your altar.
Other witches use their altars less for worship and more for magical workings. If this is the case then you would probably keep items relevant to your current spells and workings in situ. You may choose to redecorate in line with the seasons and/or sabbats in which case the stones and crystals you put on your altar will change as the wheel turns.
A less common use for the altar is simply a place of magical storage in the home. If this is how you choose to you your altar it may become a good place to store your collection of magical supplies.
I think altar usage is largely a matter of preference and as always it is crucial to have a good understanding of why you are choosing to do something. Intuition plays a large part but so does having a practical understanding as to why you are completing a specific action. Intuition is only as good as intent so think not only what feels right to you but why you are doing it. Once you have decided the purpose of your altar and what it means to you as an individual you will find the answers as to what you want to keep on it.