this sounds real nooby but do you sort of drill away a certain size hole at the top or something so that the cross bar sits 100% straight?
Yes.
T-Bars:
2 ways to do it:
*Drill a hole through the Down tube and then just slide the Crossbar through the hole and weld. This leaves a bit of the Down Tube on top so the bars are not smooth all the way across.
*Notch the Top of the Down Tube so the Cross bar rests on top of the Down Tube and then weld.
Both of the above only require a simple Jig to hold the bars in a T and keep the Cross Bar at a 90˚ to the Down Tube. You don't really need a jig but if you are making quite a few it helps speed up production. Time is Money.
Drop V and similar style bars that use 2 pieces to make the Cross bar a more complex jig is required because 3- separate pieces need to be held in place, either with no back sweep or with back sweep.
You can google Tube Notching to see how it is done with a Tube Notcher or with a saw.