Keep in mind I do not own a MEP-003a, but do own a smaller 3kw MEP-701a and have skimmed over the MEP-003a TM. First a little basic theory your generator internally is either a 6 or 12 lead reconnectable generator (the distinction does not matter for our purposes here) these leads are reconnected in various combinations by the voltage selector switch by the circuit breaker (never turn this switch with the unit running). In practical terms what this means is your generator can be set to output 120/208V Wye 3 phase power (used in commercial 3 phase equipment), 120V single phase only power or 120/240V split phase (often also called single phase) used in household electrical connections. On the generator power connector you will find screw down split lugs marked L0,L1,L2,L3, in 3 phase mode all 4 connectors are used, in 120V only mode only 2 are used, and in household 120/240 split phase 3 are used (2 lines and a neutral). This is where things start to get confusing because these military generators use a different labeling system than residential 120/240 service with its L0 (neutral), L1 (line), and L2 (line). When the selector switch is in 120/240 mode and you are wanting to connect to a residential system (through a transfer switch for safety reasons) then generator L0 connects to house L0 as neutral, Generator L1 connects to House L1 (line ), then Generator L3 connects to house L2 (line) (note the is L3 to L2). This gives you 120 Volts measured from either line to neutral and 240V measured Line to Line. Measuring these line to line and line to neutral volts and amps is what the selector switch on the CONTROL PANEL does, for single phase operation you will only use some of the possible settings for measurement. At this point you may be asking why have both a 120V only and a 120/240 single phase setting on the voltage selector switch, the answer is in 120V only mode you get access to the full output of the generator, in 120/240V mode the output is split into 2 halves with half the output going to each line output and the return coming back through the neutral, in this mode it is more important to balance your loads and so you never draw more than half the total output out of either line (again back to the use of that meter selector switch on the control panel).
Ike
p.s. another important question when wiring a generator up to a home system is the ground bonding of the neutral connection all the references in the TM will talk about grounding L0 (neutral) to the frame and to a ground rod at the generator for stand alone operation. When used with a transfer switch it may be necessary to unbond L0 at the generator from the frame, or use a transfer switch that has a switched neutral if the MEP003 will not run unbonded. The important thing here is that your neutral is only bonded to ground in 1 place (this is usually at the service entrance for a home) this is a point where you should talk over your plans with your local electrical inspector or other electrical professional as code requirements vary from region to region.