Here is the brunt of what was said in regard to coats and flags:
Coat colours are a moot point as to be honest we don't know for many regiments. Some probably didn't have any uniform at all. Blue coats were fairly common but white was less so, with some exception - most famously the Earl of Newcastles "Whitecoats" at Marston Moor (probably actually a light gray). Of course you could go for Brookes "Purple coats"! Coat colours don't correlate with flag colours either & we don't know much about those either!
Perrymans – the flag is correct but the references I think I have seen for the coats are either suspected to have been in blue or grey coats. If it bothers you I'd use you two ensigns for your next unit (ie Pennymans in blue of grey or a mix of both to be safe as ECW units weren't very often in just one uniform coat colour) and paint up two new ensigns and flags for this green coat unit.
Northamptons, TIlliers and Broughtons wore green on the Royalist side but no flags are known for these but its very unusual for flags and coats to be the same colour in ECW.
Jones Farnham greencoats are the most well known Parliamentarian green coat unit. The flags are thought to have been white. Part of Manchesters huge regiment may have worn green but there also references to it being in red and possibly blue. Worth bearing in mind coat colours can change year on year and a unit my be in green one year then grey the next. Facing colours were also almost certainly mixed in battalia.
I was actually planing on going along the lines of 'green coat = green flag, red coat = red flag, blue coat = blue flag etc'. I guess I would be wrong doing this.
How do you guys decide what flags to use with what coat colors?
Also, once you have made your flag color decision, how do you decide WHICH flags to go with. I have seen ECW units that have flags for the Colonel's Company, Lieutenant-Colonel's Company, Major's Company, First, Second & Third Captains' Companies - that would be six flags to a unit!!! I only want two, three at the most (three if I opt for command stands for each element http://saxondog.blogspot.com/2011/03/ecw.html).