The E3800 stacking i simlar to IRF (or c3750, EX-4200).
Which means you can connect your switches or servers to both switches with distributed link aggregation (DLAG). Basically you just configured it like any other LAG between the stacked switches (which acts as one switch with the physical swithces as linecards) and you other equipment.
Would you should choose depends on features, and also what other equipment is installed - from a management perspective.
Cheers