As usual the most simple tasks are the hardest on godaddy servers.
When you register a new domain or transfer an existing domain from another registrar to godaddy you probably want to point that domain to your hosting service (existing hosting server on godaddy or elswhere).
By default after transferring a domain to godaddy, the nameservers stay what they where before - you want to use godaddy nameservers and add a "A" record to point to your hosted server -
To do this you first need to perform a temporary step and to 'park' your domain with godaddy, this changes the nameservers used by your domain to godaddy nameservers.
(select your domain and choose 'nameservers' -> 'set namservers -> choose the park option)
After this you will be able to access the "Total DNS" panel controler for your domain, and there you can add an 'A' Record to point the domain to your hosting server (the web server) IP address. You can also create a wildcard subdomain to point to your web server.
[select your domain or refresh the domain page you were on before, near 'Total DNS' click 'Total DNS control' - there you will have a single A record pointing '@' to the parked IP address - edit it and change it to your web server's IP and optionally add more A recored for other subdomains you want to reference (e.g. www.mydomain.com, sub2.mydomain.com, etc ...) you can also add an A record for a wildcard subdomain *.mydomain.com to point to your web server, but then checkout my wildcard article for IIS configuration needed http://me-ol-blog.blogspot.com/2010/09/wildcard-domain-problems-with-iis-607x.html )