How to protect these NM cables?
You can't get one big one.  You'll smack into 310.15(B)(3)(a), which says no more than four circuits per conduit even if you can walk through the conduit standing up.   In residential split-phase wiring, all properly wired cables count as 2 conductors for the purpose of this chart, and 70% derate is harmless. 50% is a serious problem.  


  


Having 10 wires (5 circuits) requires a 50% derate, which requires bumping up to the next size of wire (#10 for a 20A circuit, ouch, and that takes more space which means fewer wires can fit etc.) 

Instead, switch to THHN wires inside that conduit

It looks like he used nice big pipe - either a 1/2 and 3/4, or a 3/4 and 1".  Not clear.  (a 3/4" pipe is about 1" diameter). You can easily fit 3-4 circuits in each one as individual THHN wires.  

Get some black #12 stranded THHN, white #12 also, green ground screws, and a few feet of solid #12 bare wire.  Also a 5-pack of colored electrical tape (for marking circuits).  Also some 4-11/16 large deep square junction boxes with knockouts that'll fit your pipe, and conduit knockout adapters as needed.  The big boxes are cheapest at a real electrical supply, "big box" stores overcharge for them. 


Pull the existing cable out of the pipe.  (you can do this one pipe at a time so you only knock out 1 circuit; once we've done one pipe you can put both existing circuits in that). 
Install a junction box on the end of the pipe (cut or bend if necessary) using a proper EMT-junction box fitting into a knockout.   
Do this to both ends. 
Bring the Romex cable into the junction box via a knockout, using a cable clamp of the right size, clamp it, and cut it with 12" of extra length inside the box. Shuck it back most of the way back to the clamp. 
Figure out the length of the pipe, add 24" and that's how long your THHN wires need to be. Check first, before cutting. 
Neutrals must use white THHN. (or gray) 
Hots must use black THHN. (or any other color but green).  That includes 240V circuits - so if it comes in in black/white /2 Romex, it must go through the pipe in black/black. 
Use colored tape to mark wires.  First group them by circuit (black-blue and white-blue is circuit 2), and then to distinguish hots from each other. 
Mark every circuit. Leave "plain-black" and "plain-white" for the future. 


In each box, for the Romex grounds, put a 9" pigtail on green ground screw, and attach it to the grounding screw inside the box.  Splice that ground to all the Romex grounds. The rest of the way, ground will be carried by the pipe itself.  If you don't like that, feel free to throw a single #12* bare solid wire into the pipe also. This will be redundant, but redundant grounds are allowed. 

* If there is #10, #8 or #6 wire in the pipe, the ground wire must be #10. 

Now, for each cable set's conductors, do wire-nut splices from the Romex to the THHN.  Do one circuit at a time.  It's no big deal attaching a stranded to solid wire, no need to pre-twist, just use good wire nuts (Ideal) and tighten rather firmly!  Hold the nut and yank the wire for your pull test. No need for tape; if you feel like you need tape to hold the wirenut on, that's a bad connection that will arc-fault; fix your technique instead. 

Conduit fill limits: No more than nine #12 wires per conduit. That is the limit for 1/2" conduit, but that's also where you'll hit the cubic-inch limit of those 4-11/16" square junction boxes (42 cubic inches). If you use larger boxes, you can take 3/4" conduit right up to the 4-circuit limit.

Why are we using #12 wire on 15A circuits?  Fewer wire spools to buy and less leftovers.  A 50' spool each of #12 + #14 is more expensive than a 100' spool of #12.  

Why not just shuck the sheath off the Romex cable and use it?  It's not tough enough to handle life inside conduit, it's too stiff, and it lacks the markings on the side of the wire  "12 AWG THHN/THWN-2 ABC Wire Co. (UL) blah blah" that make it legal to use.