From my experience you do not need to add the register prefix tag in the html if you are loading the controls into placeholders dynamically...
What error is it giving you if you don't add the register prefix tag?
Here is some of my code (vb)
VB Code:
aPlaceholder = CType(aSkin.FindControl("plhContent"), PlaceHolder)
If Not (aPlaceholder Is Nothing) Then
Dim leftColumn As UserControl
leftColumn = CType(Me.LoadControl("blah.ascx"), UserControl)
aPlaceholder.Controls.Add(leftColumn)
End If
aSkin is just another usercontrol on the form. You can replace it with the actual web form (ie. Me.FindControl("plhContent")).