First time when you distribute the package to distribution point then SMS/SCCM chooses the NTFS drive which has maximum free space.If you have 2 to 3 NTFS drives and you want to chosse one of them. There is no provision given at SMS/SCCM server side to prevent SMS/SCCM from using a NTFS dirve with maximum free space. Also, if any drive that is currently being used for distribution point is full, then SMS/SCCM starts using the next available drive with maximum.
Method 1:
Create the blank text file on the other drives with the name NO_SMS_ON_DRIVE.SMS which will prevent respective NTFS drive from creating SMSPKGC$ (Here C represents the drive) folder.This file named NO_SMS_ON_DRIVE.SMS needs to be placed at the root of the drive you want excluded.Drive which dont has NO_SMS_ON_DRIVE.SMS file,will have SMSPKGC$ folder.
Method 2:
Insted of installing a standard distribution point,install a distribution point on a server share.
1) Create a folder called smspkgx$ on the partition you want it and share that folder. (x is the drive letter of your choice).
2) Create the distribution point on a share basis in the sms admin console instead of on a server name. (Share has to exist). Just right-click site systems inside the sms admin console, select new, server share, ...)
REF : http://support.microsoft.com/kb/871234