Advice on best way to mold cubed object.

Normally, Bondo and standard modelling putty (Squadron, Tamiya, etc.) hold up pretty well to being molded in RTV. The only times I have had problems with those types of fillers is when I have used natural rubbers, because those need both heat and pressure to vulcanize properly. In those cases, two-part epoxy putties tend to hold up a lot better under the stress. 

But, since you are using a room-temperature vulcanizing rubber, no worries.

Thank you for all the tips. Much appreciated.

@KnightTemplar5150 - A question I have about the master. I've done a few passes of Bondo glazing putty, primer and sanding, but just can't seem to get the corner creases filled. I designed and 3d printed this so it's 6 pieces that snap together for the cube. What would you recommend I use to get into the fine gaps? 

How about doing a corner to corner casting.  That would give you two seams on the corners and two on a raised flat.  Basically an upside down triangle with square ends...easy to fix the seams when the two halves are put together.

You can do a mold of the item in silicon, cast it in wax, then make the mold from a heat resistant material, melt the wax out.  Cast in metal.  I'd make the top of the mold open and then you can square up the top on both castings, glue together and finish the seams.

If the mold is a rigid material you must leave at least some relief angle.  If the material is tflexible you do not need relief angle.  Any detail on side would lock a rigid mold.

I would recommend  a pattern of thin metal sides with the details sticking out or depress into the side, cast six sides and glue them to a wooden or plastic block. 

Your idea of molding three sides to each half of the mold is fundamentally correct, but you have a few things to consider here.

A cube isn't necessarily the easiest shape to cast in metal. Maintaining straight lines and (relatively) flat sides are key to a successful casting, but the manner in which metal cools inside the mold can cause warping and shrinkage, which pretty much defeats the whole purpose of casting the piece in the first place. You are going to need to consider making a larger mold to help insulate the piece to ensure that each side of the mold can accommodate the heat and pressure as the metal cools. Making the mold a little taller will allow you to employ a "button" to help the metal both fill the cavity and stay warm enough in the mold to set up without shrinking or warping. 

You're going to need to decide where to sprue and gate this piece for pouring. You'll also going to have to lend some thought to adding vents to the corners to ensure that the air in the mold has somewhere to go once it gets displaced by liquid metal. A larger mold will give you more options as to where you place the vents and the size of the channel.

You don't have any apparent undercuts in the photo, but your master has a lot of work left. The mold is going to pick up every single defect - the seams and cavities along the edges, for example - and these will only be magnified and exaggerated in metal. Take the time to putty, sand, and correct the defects until it is perfect. Then, prime it to double check your work. The smoother you can get the surface, the easier it becomes to mold, cast, and finish. 

Just a reminder - liquid metals don't play nicely with moisture of any sort. Don't use a liquid/aerosol mold release when you are ready to cast. Use talc.

My sincere apologies for the double post. It had been over a day and thought my first one didn't go through. Anyway, I'm going to try to post a link to the photo here of my model.