Can you please tell me how I can do the following. I'm trying to setup
a Windows Server 2003 network. I would like it if you could give me
the simplest but most effect method. can you give me information that
is specific and easy to follow.

I need two locations connected by two Windows 2003 routers. The
communication between the two locations must be secure as it will go
through a public network. One location is the Meganet.com and the
other is Suppernet.com.

1) Meganet.com hosts the SOA for both locations. However name
resolution should take place locally on both locations.

2) There is a R&D department at both locations.

3) Suppernet.com also has a manufacturing department. Each department
should be managed locally (not centralised).

4) Shared folder Dev which resides on the Meganet.com location must be
easily accessed by the R&D people on both locations.

Meganet.com

1) There are two file servers that should have documents for the
maintenance department. These documents should be easily accessed by
all maintenance people. Clients must have access to these files even
if a file server should fail.

2) The maintenance team run very specific applications that require
the schema to be changed. However the R&D department in Meganet.com
also run a specific application that is not compatible with the new
proposed schema.

3) The R&D department on the Suppernet.com site must be managed by the
manager of the R&D department on the Meganet.com site.

Suppernet.com

1) An image of XP should be available for clients to install using
RIS. This simple XP image should be fully automated and name the
computer automatically starting the name with SecureNet.

2) There should also be an image of Windows XP and Microsoft Office
available for installation by RIS. All computers installing this image
must be named automatically starting with the name DEV.

First of all this is a very broad question. I'll do my best to give
you enough information.

Meganet.com

2) Are we talking Active Directory Schema? If we are it's kind of
interesting that certain software would change it to that extent. I
personally wouldn't have bought it or installed it. :>

Your site setup and layout clearly would need two seperate domains.
With two DNS servers and two ras servers. 
You could run Windows VPN services for your secured connection between sites.
As far as RIS goes this is an excellent walkthrough for the images themseleves
http://www.mcmcse.com/microsoft/guides/ris.shtml
For the addition of Office, have you thought about using a GP to
install this instead of RIS? It works a lot better that way.

For the cross site access using two seperate forests and domains, you
would need to setup a two way transistive trust. This is a lot easier
in 2k3 than NT4. Plus this would bive you the needed seperate
Scheme's. Manurfacturing users in one and R&D in the other. Next comes
the question of whether the company's would mind their users have the
other company's name such as jdoe@meganet.com when he is actually
works at suppernet.com.