Custom Eagle CAD part for Arduino Pro Mino
You are designing the symbol, not the package.  The symbol is what will be inserted into the schematic.  As the name implies, it is a symbolic representation of the part.  The physical layout of pins should have nothing to do with how a device is represented in a schematic.  That only matter in the package, since that defines the mechanical layout on the board.

No, don't ever put pins in the middle of a symbol like that.  A schematic must be clear and easily allow others to understand the circuit it is trying to communicate.  Making a mess as you are proposing goes against that purpose.

Forget physical pinout and pin order when making the schematic symbol.  Place pins by function.  Try to put power connections at top, grounds at bottom, input-only pins at left, pins of a sub-function together, etc.

Above all, don't make a mess.