You didn't give much information regarding your environment, so some of the responses below are based upon assumptions: that you manage all devices that are connecting, that they are joined to your A/D domain and that you are using the Windows supplicant. You haven't said what version of Windows you are running and what version of FreeRADIUS you are running!
Currently with Windows machines I can't just connect to the SSID and enter in a username and password. I have to go and manually add the SSID, modify some settings;
If you are referring to PEAP vs. TLS, that's a Windows XP issue. XP defaults to TLS and won't connect automatically if you are using PEAP. However, you can push wireless policy to your Windows devices using A/D group policy and set this up automatically.
specifically turning off validating server certificate
This is a bad idea as you could be passing your credentials to someone else's RADIUS server. It's best to generate a certificate signed by an internal Certificate Authority and require a cert signed by that CA in your 802.1x config. This too can be pushed to Windows devices as part of your A/D policy assuming they are joined to your domain and run Windows.
turning off automatically use my Windows login, and turning on User or computer authentication mode.
Why do you want to use manual authentication as opposed to automatic? If the machines that are connecting are joined to your A/D domain, you may want to consider using machine authentication. User authentication, in the current release, doesn't support MS-CHAP password change. Also, user authentication with the Windows supplicant requires the presence of cached credentials (because you logon locally first and then connect to the wireless network) which may not match current A/D credentials.
error messsage was: winbind client not authorized to use winbindd_pam_auth_crap. Ensure permissions on /var/cache/samba/winbindd_privileged are set correctly.
Use "sudo wbinfo" or run it as root if you don't use sudo. That said, wbinfo isn't used by FreeRADIUS to authenticate to A/D (ntlm_auth is used for PEAP/MS-CHAPv2).