Don Sebastian,
All of the information is free on the net from primary sources, but it's almost all in 16th century French. If you speak French it's not so bad (except of the proliferation of X's instead of S's, especially from Western French writers. This period is poorly served in English, unless you read Sir Roger Williams bit of the war he was involved in.
Then there's the digging. There's not much direct talk of organization except from military writers, and they are usually trying to push their new or theoretical organizations, such as De La Noue here:
link
Regiments were of course composed of companies, and writers would often count companies rather than regiments, sort of like 'there were 14 companies of Gascons' rather than saying one or two regiments. If five companies of Englishmen were present, you had a five-company regiment unless say, the Huguenots would lend them two companies of shot to bolster the unit.
The details are anecdotal, often about a specific battle. So D'Aubigny in his Histoire Universelle might tell you how many pike vs shot there are in the Huguenot infantry regiment at Moncontour, but again that's the way the captains arrayed them at that battle based on what was on hand. There was tremendous flexibility and the captains had a lot of say- so they might brigade horse into large units of 1500 men or break them up into tiny ones of 200.
Even royal units like the Legions with more fixed company organization were fielded as necessity required, like in the bizarre terrain at the battle near Lucon (Saint-Gemme) in 1570 which again was fought with infantry in smaller groups.
Finally, armies made big use of picked-men with special task, making units of 200 or even several thousand- usually shot-armed troops but even pikemen on occasion, like the 200 man Spanish vanguard at Heiligerlee in 1568.
So while armies had complex organizations and structure, they were the outward form but rarely the reality, being mostly regional and decentralized. A company that was supposed to be three hundred men, 200 of them pikemen might be raised as 150 arquebusiers because no harness was available to raise pikemen and there were not enough recruits.
Anyway, here are some books you can find online. Maybe you can find a copy of them on archive.org that has them in text instead of scans and try google translate. Not perfect, but better than nothing:
To start you off, here is Francois de la Noue Discourse in English; while a lot of new theory, it's got lots of anecdotes:
link
Also in English, Montluc's commentaries
link
In French:
Histoire Universelle- Agrippa D'Aubigny
Histoire de France depuis l'an 1550 jusqu'à ce temps -La Popeliniere
Mémoires de la vie de François de Scépeaux
Vie des hommes illustres et grands capitaines français- Brantome
There are more (Estoile, Sully) but these are probably the best. For the Spanish side of things, get Mendoza.
I hope this helps,
TPC