I just finished setting mine up and i kinda had the same problem. i only got the 13in macbook pro so i only have two thunderports but i'm also using something similar to what the first commenter posted.
it has two thunder ports that you can use for your a) charger and b) ethernet adapter. there are similar that have the ethernet port within the hub but i don't need that so i wasn't looking for it
i have ^that^ plugged in for my HDMI cable (separate monitor), my laptop charger and for this
this is a splitter but it's powered through an outlet and then connected via usb to the hub that is in the first link. I have my external HD, MPK Mini II, Pioneer DDJSX2 and focusrite scarlett 2i2 connected to the *powered* USB hub and haven't noticed any delay issues of the sort. I feel like the USB Hub being powered on it's own before even being connected to your laptop helps with it? i did some searching on the answer and everyone basically said the same
anyways i hope this helps. this had helped me minimize my wiring and such. hope it can help you!
EDIT: **