See if someone hasn't already done it:

http://office.microsoft.com/en-us/templates/FX100595491033.aspx?pid=CL100632981033

the template gallery.

also, search google for house estimating excel  (or refine you terms)

The first step is to sit down and develop a 'specification' for the program.
What information is going to be available in the program?
What operations does the end user need to be able to do with the information?
How is the manipulated information to be presented to the end user?

Then your next job is going to be to get a list of all potential materials
and their pricings and put them somewhere for reference.

You say you have 2 files now?  What kind of files are they?  I presume that
one file contains the list of materials and sizes while the other list
contains price list?  How do the two lists relate to one another?

The easiest thing to do is to use one worksheet for materials and unit price.
So you would have various grades of lumber and the cost per board-foot,
sheetrock and the cost per sheet, etc.  The second worksheet would just have
the amounts of material needed.

If I were to undertake such a project, I would begin with a bill of
materials.  Concrete Block, cinder block, lumber, poured concrete, fasteners,
re-rod, etc.  I would not worry about quantity in developing the bill of
materials, but bear in mind that quantity is essential for future
calculation.  The next thing would be to establish a unit of measure, ea for
each, bf for board feet, etc.  which will be needed when quantity is applied.
I would set up the program so that the bill of materials could fluctuate in
length and content, since you would never know what an architect would put
into their design.  This should run about 1000 hours of development time,
counting of course the research to establish the measurements, etc. Unless,
of course, you assume that you will always have a bill of materials from the
architect at the time the estimate is made, in which case, the architect has
probably already done the estimate for materials.

Then I would set up a manpower estimating program, based on skills required
for the particular structure.  This would include carpenters, masons,
electricians, plumbers, specialists, platerers, drywall hangers, laborers,
etc.  I would try to establish a median wage scale and then add in a standard
figure for overhead, g&a and profit.  I would attempt to research for
information on some kind of expected production rate for each skill level so
I could set up formulas for blocks per man hour, board feet per man hour, etc.

Well, this should get you started.  I am sure we will hear from you again.