Hi Seung Lee,

I'll give you some of my opinions in answer to your questions, there's no real best answer, and others could have different views.

Q.1

I would get them to generate the construct into a cloning vector first, then clone it into your vector of choice (further thoughts on vectors in Q.2). You should get them to supply both vector constructs, so you have a good source vector for your future work, and an expression vector to start working with immediately.

Q.2

By choosing the standard sub cloning route, you can specify/provide from a greater range on expression vectors, than their Express ones. Which are the best is a complex question, depending somewhat on your protein, end requirements, planed experiments, tags, expression systems etc. If you are thinking of using E.coli (as you mention RBS) then the pET system is a good place to start, I recommend you do some reading up on it before choosing. One point I'd add is to use vectors with Kanamycin resistance over ones with Ampicillin.

Q.3

Unless you have a very good idea about which promoter & RBS you are wanting to use I'd just have coding sequence synthesised, then you can add it to vectors that already have established good transcription machinery. If you want a specific promoter later that's not available in a vector then you can always have it synthesised.

Q.4

Which enzymes to use is almost impossible to answer, as it will depend upon what you are planing to do. For example: one useful 5' enzyme is NdeI as it's recognition sequence CATATG allows direct cloning at the start codon - useful for many of the pET vectors - however if you are planing to express in mammalian systems it is a bad choice as it would create a poor Kozak sequence.  It's more important not to have any/many common ones in your gene so that you don't run into any complications with later cloning.

Q.5

The only ones I'd suggest might be worth it are subcloning (depends upon your experience & time) and plasmid preparation if you ever require mg quantities of plasmid DNA (generally for large scale transient mammalian expression).

Note: these only scratch the surface of the topic, expression of proteins is generally  much more complex than it first seems.

-Richard