My buddies and I are completely new to most of these mods and some to factorio in general.

We spent about 4 hours today playing with the pack but could not for the life of us figure out the stacking on belts.

We found the stacker, we found the upgrade to stack specific items. Were able to stack on the belts but the machines / furnaces wont take stacks. So we had to stack to compress, push down the belt and then unstack to uncompress.

Are we missing something?

That is exactly how it should work, the stack is a different item, and it must be unstacked to be useful.
The main use of the stacker is to increase the throughput of your belts