It was all in his head
I think all the main characters were his internal dialogue (self talk).
His boss was his parent(rules to live by).
Management was his adult, objective self (processor of information, zero emotion).
Bob was his childish influence (anything goes, I want it now mentality).
His pain, like most people, is caused by conflict of the parent and child in his mind.
"Zero theorem" is a paradox. The only way to make zero 100% is to destroy everything known to you and your being.
100% of zero is zero. Void.
The conflict is resolved at the end when he's at the core and it self destructs, in effect destroying his former self (thought patterns).
This is symbolized when he looks into the void, sees pictures from his life and the galaxy/black hole. At first he's scared of the uncertainty of himself (is he real?) and steps away.
However, he's ready to "step into" the next stage of his life/being/entity and unafraid, smiles and takes the plunge.
He ends up at what was the only place he was happy in the film/life, the beach.
I'd say the main idea is that your "life" is all in your head.
It is what you want it to be.