So Im going to be starting bonsai from seeds and I need help. I bought two types of seeds:

Acer Palmatum Atropurpureum
&
Cryptomeria Japonica

Is there anything I need to do to the seeds before I plant them and when I plant the seeds do I start using fertilizer immediately?

The seller did nopt give you information?

I would say this is about the worst time to start from seed. The seedlings do not have enough time to grow till winter.

That being said..
www.growingbonsai.net/germinating-treeseeds/

The website said that for the japanese maple seeds I should put it in a "cold stratify for 60 days " how do I do this?

And for the japanese cedar it says to " Soak seed 24 hours in water
Place seed on a moist paper towel and fold over or sow as normal in container.
Put paper towel or container in a plastic bag and place in the refrigerator for 4-6 weeks.
Remove to warm area and await germination. " So after letting the seeds sit in cold water for 24 hours I just put them in a damp paper towel and then in the fridge and I leave them for 4 - 6 weeks?

You said its the worst time to start from seed. If I follow these instructions would I be able to plant right away?

Satans_Organic_Puppet wrote:

The website said that for the japanese maple seeds I should put it in a "cold stratify for 60 days " how do I do this?

Like this:

Satans_Organic_Puppet wrote:

Soak seed 24 hours in water
Place seed on a moist paper towel and fold over or sow as normal in container.
Put paper towel or container in a plastic bag and place in the refrigerator for [60 days].
Remove to warm area and await germination.

Satans_Organic_Puppet wrote:

So after letting the seeds sit in cold water for 24 hours I just put them in a damp paper towel and then in the fridge and I leave them for 4 - 6 weeks?

Yes.

Satans_Organic_Puppet wrote:

You said its the worst time to start from seed. If I follow these instructions would I be able to plant right away?

You would be able to plant straight away but the problem Leatherback was talking about was that the trees will not have enough time to grow before winter.
The only way I can think of to remedy this is to move them indoors over winter, put them out in autumn and hope they survive.

Ed