Firstly, if you don't know how to do it, here is an explanation of how to change formation in game without pausing.
01. Set up your default formation just as you normally would. Make sure every tiny detail is perfect. Set individual attack and defence arrows. Pick your best team, this may not be final until you have finished Formations A and B.
02. Go into STRATEGY, You will see
MANUAL
SEMIAUTO
FORMATION A
FORMATION B
COPY TO A
COPY TO B
select MANUAL, then assign Triangle to Formation A, and Square to Formation B. Assign X to Counter Attack and Circle to whatever you want.
03. Then select COPY TO A+B. This will give you a template to work on for your alternate formations.
04. Go into FORMATION A and move your players around to whatever you want. Alter attack and defence arrows as required. Try not to pull too many players out of their default positions, a couple of subtle changes can have as much impact as a full formation change. You need to take into account your players abilities and what other positions they can play. Do the same for FORMATION B.
05. Now you're ready to test it out. Use Exhibitions until you find the right balance, so you don't mess up your league if it isn't working for you. To activate the formation changes in game, you need to press L2 + Triangle or Square. When the symbol appears next to your status bar, it means it's active. Don't have both on at the same time though, they'll cancel each other out.
06. Practice and experiment. That is after all what gaming is all about.
OTHER NOTES.
Instead of having 3 formations, you could go for a simpler option of just 2. Instead of selecting MANUAL, select SEMIAUTO and assign L2 to FORMATION A. This way you only have to press L2 in game to activate your formation change. And it makes using the other strategies, like counter attack and zone press easier as all 3 will be automatic. Although the hardcore won't like the idea of the computer changing for them.
Player selection and positioning is key. You may need to edit some players to compensate for extra positions Konami didn't get right.
Your formation will only be saved in your master league if you have done it within the menu system, and not before a game. If you do it before a game, go to stock formation to save it.
Don't forget to save it.
All the details you could need are on the images.
HIGH NORMAL LOW (blue text) = individual defensive status (blue arrows). Accessed with Formation, Individual.
Earlier pictures were made for PES3, later you will see a new design, they are for PES4, but the idea carries through both games.
Enjoy.
Attacking Options