In Strategy Desktop, project can be registered through Project Monitor under 'Administration'.

Project 'Sales Analysis Module' is registered after clicking the checkbox besides project name.
The project can also be registered by using Strategy SDK. The key API call is IDSSProjectReferences.Add().
The following sample code explains how to register 'Sales Analysis Module' project on Strategy Intelligence Server 'MSTRServer'.
'--------------------------------------------------------------------------------
' Create a new DataSource connecting to existing IServer
Dim MyDataSource As New DSSDataSource
MyDataSource.Type = DssDataSourceTypeServer
MyDataSource.Location = "MSTRServer"
MyDataSource.Mode = DssConnectionModeServerAccess
'--------------------------------------------------------------------------------
' Login into data source
MyDataSource.AuthMode = DssAuthStandard
MyDataSource.login = gLogin
MyDataSource.Passwd = gPassword
MyDataSource.Init
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'Create a session and connect to configuration
Dim objSession As IDSSSession
Set objSession = MyDataSource.CreateSession
Dim mobjObjSource As IDSSSource
Set mobjObjSource = objSession.Component(DssRoleConfigurationSource)
Dim MySource As IDSSSource
Set MySource = objSession.Component(DssRoleObjectSource)
Dim i, j, k as Integer
Dim oConfigRoot, oServDef As IDSSFolder
Dim oServ As IDSSServerDef
Dim oProject As IDSSObjectInfo
Set oConfigRoot = mobjObjSource.Configuration.Root
Set oServDef = oConfigRoot.Item("Server Definitions").Special
'Strategy BI Developer Kit refers to the name of the server definition name given in the Configuration Wizard Set oServ = oServDef.Item("Strategy BI Developer Kit")
'--------------------------------------------------------------------------------
'search for 'Sales Analysis Module' project
Dim myProject As IDSSProject
Dim mySearch As IDSSSearch
Set mySearch = MySource.NewObject(DssTypeSearch)
mySearch.NamePattern = "Sales Analysis Module"
mySearch.Types.Add DssTypeProject
mySearch.Domain = DssSearchRepository
Dim myResult As IDSSFolder
Set myResult = mySearch.Execute
Set myProject = myResult.Item(1)
'--------------------------------------------------------------------------------
'register 'Sales Analysis Module' project
Dim myProjectReference As IDSSProjectReference
Set myProjectReference = oServ.ProjectReferences.Add
myProjectReference.ID = myProject.Info.ID
myProjectReference.Name = myProject.Info.Name
myProjectReference.LoadFlag = DssProjectLoadActive
myProjectReference.MetadataVersion = DssMDVersionMD7
oServ.Info.Save
'--------------------------------------------------------------------------------
'Apply these changes
Dim objMyserveradmin As IDSSServerAdmin
Set objMyserveradmin = objSession.ServerAdmin
Call objMyserveradmin.ApplyRunTimeSettings