Your questions are very broad and therefore difficult to respond to effectively.
Reading your post I'm afraid it isn't clear to me what you are trying to achieve because I can't really get my head around your environment.
So let me try and read back what you've written and see if I'm close:
Exchange 2003 is running as domain.local, but when users send email from this sever it is sent out as from domain.com?
Incoming mail (to domain.com?) is sent to an ISP? Your Exchange 2003 server grabs this mail for your users via a POP connector?
You have another site (location.domain.local) of 15 users that don't use the Exchange server and who go directly to the ISP via POP accounts to retrieve their email(from domain.com?). How do these users currently send mail?
You could certainly install a Scalix server to act as a mail server for those 15 users, you could also probably use some other software (procmail?) to populate the mailboxes on the Scalix server with mail retrieved via POP from an ISP.
Then you lose me....
What do you mean "route the invalid recipient on the same domain to the exchange server"? Do you mean have the users on the Scalix server be able to send mail to users on the Exchange server directly and vis-versa? If you do then, of course this is possible but you'll have to come up with a routing scheme to ensure that mail is directed to the right place, i.e. when do I send to the Exchange server, when does it go to the ISP. Maybe the Exchange server becomes your internet gateway and you route everything to that, it delivers mail to local users and other external mail goes out to the ISP, and mail for the users on the Scalix server gets sent there. To have this work effectively you'll need to define and then implement an effective routing schema.
Then you lose me further...
Is site2 the secondary location and site1 the Exchange server?
If it is then we do not provide the ability to share folder access in a hetro-geneous environment, i.e. and Exchange user can not access a shared folder on a Scalix server and vis-versa.
Public Folder access is possible, but this involves replicating the data between the public folders by giving the Public Folder a mail address and then having additions to the folder sent to the other machine. This doesn't handle deletions/modifications to items in the Public Folder.
I'm sorry, but I simply can't answer:
What kind of issue should I be ready for.
without knowning a great deal more (beyond the scope of community forum support) about what you are trying to do and your environment.
How hard is the implementation and are there step by step guide to do the installation.
Again, sure we have an installation guide and Scalix can be simply installed. We don't have a step-by-step guide detailing how to do your specific implementation. What you are trying to do sounds possible, but it sounds like you really need specific implementation expertise to set it up for you, or you need to sit down with the product and manuals and work it through yourself.
Scalix is a Linux application, you say:
I dont have much experience with fedora
You don't say how Linux/email savvy you are? If you aren't familar with email conifguration (sendmail, DNS, MX records) then I think you are going to struggle to create the solution you are after even if we can help you get the Scalix configuration sorted out.
Cheers,
JG