Its probably really bad practice to have email addresses with subdomains in them.
For one, it could cause errors with your users registering for site's with the new email address. Could lead to validation errors, typos, and build lots of headaches.
Your smartest bet is to invest in multiple domains user@yourcompany.com and user@yourcompany.co.uk
You can have all your folks on one domain, as a third option. You could use two email servers or just setup email forwarding from google apps to godaddy for the ones that will stay on with godaddy.
Here is how you do it for your scenario (the one described above)
Make an A record for each domain.
us.company.com - 127.0.0.1 (use your ip)
in.company.com - 127.0.0.1 (use your ip)
Then id make two more a records
mail.us.company.com (ip of godaddy mail server)
mail.in.company.com (ip of your mail server)
Then you make your mx records
The mx records will be.
us.company.com going to mail.us.company.com with priority of 10
in.company.com going to mail.in.company.com with priority of 10
Again the above approach is not the cleanest way of doing things, and can lead to problems with some mail servers, scripts, sites, ect.
Best of luck.
PS. if godaddy does not allow you to setup DNS records the way you want, try Zerigo DNS they are great. And for a GREAT alternative to google email apps check out Rackspace hosted apps. They have AMAZING Support. I use them for Both exchange email and standard pop email at my domain and could not stop recommending them!!!
Here is the above sample for Zerigo with the domain name Pickle.com
us.pickle.com
MX 10 15 minutes
edit
clone
delete
mail.us.pickle.com
mail.us.pickle.com
A 15 minutes
edit
clone
delete
127.0.0.1
mail.in.pickle.com
A 15 minutes
edit
clone
delete
127.0.0.1
in.pickle.com
A 15 minutes
edit
clone
delete
127.0.0.1
us.pickle.com
A 15 minutes
edit
clone
delete
127.0.0.1