I recently setup an Integrated Dynamics storage system, and whenever I shift+left clicked an item into the grid, it first went into the crafting grid, then if that was full my off hand, and if that was full it shuffled it in my inventory. It worked when I shift+right clicked an item, but upgrading all the Integrated Dynamics mods, Cyclops Core, and Common Capabilities to the latest versions let me shift+left click correctly. I have not tried anything with Evil Craft yet, but as it depends on the Cyclops Core as well, it might have to be upgraded too.

Mods have been updated so I assume this is fixed in 1.0.0.