I personally wouldn't run Multiple D because none of the formations are as developed as they are in their parent book (43, 34, etc). If you are set on being true to life, I will let you know how I ran it a few years ago.
The bottom line for recruiting is that you want linebackers, lots of them.
Your defensive ends should be run stoppers, I personally just recruited defensive tackles and ran a 3 DT front in the 3-4 and then put the #2's at DE and DT on my depth chart as defensive ends. So I could use my DL Sub package in 4-3 to have a 4 DE front, which Bo Pelini used extensively on 3rd down at LSU.
Your OLB's should be either fast DE's or big OLB's, at worst, get one of this type of player and play him on the short side on the field. The most important attribute here is tackling, with power/finesse moves being important as well.
At MLB, I personally put large strong safeties at MLB since I only used them in coverage. Think the New Mexico Lobo-back system that Urlacher ran a long time ago. A big safety that just roams all over.
Corners and safeties should be recruited as normal, preference on coverage.
What I would end up with would be three packages, all able to be run via package changes on the formation screen.
My base formation for 3-4 was:
CB-FS-SS-CB
OLB-SS*-SS*-MLB/OLB1
DT-DT-DT
My base formation for 4-3 was actually my "Quick" Package (using LB Pass Rush package in game):
CB-FS-SS-CB
ROLB2-SS*-LOLB2
OLB1-DT-DT-MLB/OLB1
I then had an Express package for both, using DLine Sub:
CB-FS-SS-CB
OLB-SS*-SS*-MLB/OLB
DE-DE-DE
CB-FS-SS-CB
OLB-SS*-MLB/OLB
DE-DE-DT-DE
I know this all sounds insanely complicated and I'm sorry for that, it got a little out of control since this is a very complicated D to run if you want to make it useful.
The bottom line is that you want to recruit a lot of linebackers, either converted from DE or Safety or just good solid LBs. I ran 3-4 as my primary defense, especially for run stopping which seems silly but it worked out. My 4-3 was actually my quick pass rush look with my LB's down at DE, so it was almost a 2-5-4 look. For obvious passing downs, I would run Nickel 335 or Dime with my Express package in, all DE's across the D-Line.
Let me know if I need to clarify that, it started to run on, sorry lol