Need Help - Planting under oak trees - root problems!

I recently designed a meditation garden. We turned an old timber sandbox into a raised deck and will have plantings around the border of the deck/ sandbox. To the side of this is a large oak tree and some smaller oak trees belonging to my neighbor on the other side of fence behind the garden.
As I started to dig the first hole - probably the biggest (for a dwarf japanese cypress) I hit a large root from my neighbor's oak tree (probably 3 inches thick). I did some online research to see what to do about this and this is some of the info I found:
1. If the root is cut, more roots will grow back in its place putting the new planting in danger.
2. It could cause the tree to die
At the same time I found more discouraging info:
1. Never amend soil under an oak tree (I was planning to do this to make my new plants happy!) The amending wouldn't be right under the oak tree, but it would fall under its canopy)
2.Plants under an oak tree will die due to soil drying out - if you water the plants it is then not good for the oak tree.

I am now very discouraged and confused - and have already spent a lot of money on the plants I will be placing here (the dwarf cypress a scarletta leucothoe, sun and substance hosta, blue hosta, coral bells, and a russian carpet cypress)
I would really like some advice on what to do about that big root and any others I might encounter. Any other input on the other concerns would be great as well.
Thanks for your help!

Here we found the "pockets" between the big roots and raised the planting area, taking care not to bury the existing roots.Do not cut through any large roots and do not add more than a couple inches of mulch over the large existing roots.
Here is some info for you.

http://forums2.gardenweb.com/forums/load/trees/msg0422033023942.html?4

http://www.lesslawn.com/articles/article1038.html

http://www.ehow.com/how_7688553_plant-garden-under-oak-tree.html

http://www.essortment.com/create-flower-bed-around-tree-66183.html

We did something similar and have been able to grow pachysandra, hosta (of course), brunnera and cranesbill geranium. Some of it is trial and error, of course, as we had to move three "Big Daddy" hydrangea because they just were withering away--the tree taking all the water.

Thanks for the replies. I have serious regret now about some of the pricey shrubs I got. I guess I could scale back to just the hostas and coral bells and find another use for the other plants.
I was also going to use stones for mulch. Would this also be bad for the tree?

Just don't bury the roots, especially any large ones close to the surface. The rule of thumb is no more than 2 inches of any kind of mulch over existing tree roots. the roots closest to the surface are the feeder roots and they will smother if too much is piled on top of them. Your pricey shrubs could go further out toward the dripline of the tree...maybe create a semi circular seating area facing in toward the trunk.

I feel for you! I have 20 oaks surrounding my house. I just installed a vegetable garden and I am starting on a butterfly bed and have run into huge roots. I knew they were from the oaks but I just tore them out. I didn't do any research as you have done. I tilled the vegetable bed back in April and I haven't noticed any problems with the nearest oaks so far and the veggies are coming in nicely. Some of the oaks are too close to our house and septic tank so we'll have to take them out anyway.

I should also mention that my veggie beds are raised 6 inches.

Not saying that you necessarily will have problems, but with old established trees if you mess with their root zone in a way that's detrimental to their health, the problems can take a while to show up so if you just did these things in April it would still be too early to tell if it's going to be bad for your oak or not.