I have data with Treated and Control and three time-groups within each.
I want to compare across the time-groups for Treated vs Control.
How do I set up my desing matrix?

    groupTC = c("C","C","C","C","C","C","T","T","T")

    groupTC_Time = c("Early","Early","Mid,"Mid","Late,"Late","Early","Early","Mid,"Mid","Late,"Late",)

I want to compare Early vs Late and Early vs Mid for Treated vs Control?.

Have you read the limma User's Guide? Section 9.6 specifically deals with timecourse experiments.

I usually advise people to setup the design matrix in the standard way, as in Section 9.5.2 of the User's Guide:

Group <- paste(GroupTC, GroupTC_Time, sep=".")
Group <- factor(Group)
design <- model.matrix(~0+Group)
colnames(design) <- levels(Group)

Then use makeContrasts() to make whatever comparisons you like.