I build them as LFE-engined vehicles, add a tonnage adjustment if appropriate using the Other Equipment section of the Armor & Misc tab, then hand adjust the C-Bill cost and free item slots when I output the stats. If I need heatsinks beyond the 1 provided by FCEs, but less than the 10 provided by the LFE, then I add them to the tonnage adjustment above, likewise any power amp. Occasionally I hit slot limits, but I can sometimes get around that with custom armor, or some hand tweaking.
EDIT: And to add to the above, a FCE is generally only 0.5t lighter than the same rating LFE and its shielding., hence why I chose the latter engine type..