The kind of airplane is irrelevant. The "kind" of PIC time is irrelevant, too. The FAA only has one classification for PIC. There's no such thing as "sole manipulator PIC", or even "PIC while wearing a Red Shirt and Dating a Girl Named Sally." Just PIC.

Whether the airplane is single pilot or multi pilot by certification is largely irrelevant. You're in the airplane because the employer put you there. If you're involved in an operation that requires more than one pilot (by type certification or by the rules under which the flight is operated), then you can log it. In this case, you can log it as SIC, if your company has a SIC program, and you're operating that flight in a multi engine airplane under IFR.

If your company requires you to do work for the company, whether it's flying passengers to Poughkeepsie, or traveling back empty in your birthday suit while smoking a cigar and inverted, it's duty, which means, along with an airplane maintained on a 135 certificate under a 135 maintenance program, that you're still on a 135 leg...passengers, cargo, or not. Industry wisdom has long perpetuated the notion of "Part 91" legs...but if you're performing duty for the company, it's duty time, and you're still 135, whether the company chooses to call it 91, ABC, or Bobsyouruncle452. Future employers only care if you were a qualified Pilot in Command, and if you list your work history as a SIC for Bobsyouruncle Airways, and you've logged PIC time, you've got some splainin to do, Lucy. The industry is as much about avoiding the appearance of evil as it is about being evil, so plan accordingly.

If you are going to log those "Part 91" legs as PIC, then just log PIC, not "sole manipulator PIC" or some other creative category like "hairy chested PIC" or "Inverted BackCourse So I Could Get Normal Sensing PIC." The latter would be neat, though. Of course if you upgrade, nobody is going to go back to count flights to see which of the nine hundred legs you flew was done before, or after your upgrade, or which ones were 91, or sole manipulator, or manipulator with assistance, or whatever the case may be. If you keep one column in your logbook, PIC, it's a lot cleaner, raises a lot less questions, and doesn't look like you were trying to pad your logbook by inventing categories of flight time.

You said it's a 135 operation and you only fly the "91" legs. Why is that? Are you not a legal crew member?