Pattern swatches, effects, and brushes can all be pains when it comes to separating but with a little wrangling, and using v10+ you can get em to behave.
When building a pattern with diagonal shapes it can be tricky to get em to tile correctly. The trick to this is manually build a grid of 9 (3X3) patterns. Draw a perfect square over the center one, select all and trim. Ungroup and grab all the new shapes inside the square area and drag that to your swatches.
As far as seps, it's time to meet my new best friend, transparency masks!
This little gem of a feature lets you spot, well, anything. You may have to make a few extra copies of stuff but what the hell, at least we are printing eh?
Simply build what ever in shades of black and group them. Then drag out a square tightly covering the object(s), give it a spot color and send it below. Now select your greyscale group and your new square (which is behind the group) and in the Transparency palletes drop down menu select Make Opacity Mask then check both the clip and invert boxes. Booya, the black and white is now shades of your spot square. Click on the thumb on the right side in your transparency pallete to edit the black and white shapes and click on the left thumb to go back to normal editing. You can even do this with multiple spot shapes so like you could have a different colored square for each bar in a bar graph.
Another trick if your printing 4 or less colors is force every elements color to one of either Cyan, Magenta, Yellow or Black. So say if you need some text with PMS 185 and its drop shadow needed to be PMS 285 I would just color the text 100% magenta and color its drop shadow 100% cyan, then just relabel the seps after they came out.
"Great spirits have always encountered violent opposition from mediocre minds." -Einstein
