Making it as simple as possible and avoiding all the complicated stuff the basic unit would have been a companie with a company banner (the square type), normally taking the colours of the lord. A companie would have been commanded by a Sergent or Vinter and would have a banner bearer bearing the companie banner, usually the small square ones featuring the livery of the lord the companie belonged to and a device to show which company it was.
There is sparse evidence on the actual troop types in companies. Some sources point to companies being a mix of troops, usually a melee type troop and a missile type troop, though this is contested, on the wargames table it is far easier to represent a companie using one troop type. The troops within the companie varied depending on what troop types the lord could muster and the money he could afford to spend on them
Companies would be under the command of a noble (lord, Knight)
The Noble would usually keep a retinue of trained men who fought with the lord.
The Noble would have a banner bearer following him during the battle to mark his position on the field who would fly a pennant (the really long triangular flags) Sometimes there would be a banner present to all of the companies under the Noble
Nobles would form their companies into battles, In the wars of the roses a system of 4 battles was normally used, with the strongest being the Commanders battle with was the 'main', then you have the 'Van' and the 'rearward' battle.
The you have the Commander, who again would have his own pennant, with his retinue, which may have had a banner.
Each Noble would have been able to identify at least the nobles flags on their side so with a glance they could who was where,
So, there were many banners, all important and denoting much useful information.
I hope this helps regards to banners. I also recommend the following link for a few banners and Pennants.
http://www.warflag.com/flags/medieval/wotr.shtml
A lot of the armour in the wars of the roses would have been the same style, maybe even some hundred years war vintage would have been utilised. One thing is certain though, not shields (other than the buckler and wicker shields of the Kerns) and no Great Helms were used during the wars of the roses. Sallets, Kettle helms, Barbutes, War hats etc are the way to go for headgear. We could go into the difference in clothing but it isn't worth it for 28mm models.
If you are having trouble try clicking on the link in my signature and checking the pictures. I re enact the period and my groups website has many pictures that may be of help.
A lot of the research done on this subject is guess work and is based on Formations of the 16th and 17th century, so be careful where you tread.