Always get the best (hottest) possible signal in the analog domain. With 4-track tape your pretty safe regarding unsuspected transients, so yeah, max out the Fostex and set the E-mu analog input gain as high as possible without clipping. Just record this signal in Cubase without touching input gains or whatever. Make sure to record to a 24-bit file.
A tip for alignment later (I believe you transfer 2 of 4 at a time): Get a high transient sound (like a handclap or such) at the start of all 4 tracks of the same recording; this will make alignment in Cubase much, much easier.