You must set the order of your imported files so that your User Constraint Files are imported AFTER all other files (HDL files, netlists, other generated constraint files, etc.). Files are imported from top to bottom, so files at the bottom of the list are imported LAST.
User Constraint Files are any constraint files you created. Tool Constraint Files (TCF) are automatically generated by a tool (SDC files and GCF files are often tool-generated). If you are using the PALACE tool, here is an example list in the proper order:
top_palace.edn
(source file)
top_palace.sdc (TCF)
top_palace.gcf (TCF)
my_constraint.sdc (UCF)