God can still be Sovereign and permit his creatures to make decisions to do though, and still be seen as part of His Plans and purposes, correct?
Methinks I should slow down a bit since it seems that you are not grasping some of the basic doctrines and concepts of biblical/Reformed theology. So, here goes...
ALL THINGS/EVERYTHING has been ordained by God. And whatsoever He has decreed/ordained He brings to pass via His perfect Providence.
Man was created as a FREE AGENT, i.e., man was given an intellect, emotions and a will. The will of man is totally dependent upon the intellect and/or will. The will is NOT independent, i.e., able to function on its own. In the beginning, Adam was created with a holy disposition toward God. There was no propensity, inclination to do anything contrary to what God commanded. However, through the ORDAINED instrumentality of the Evil One (Satan/Devil), Eve was deceived and then influenced Adam to sin along with her and transgressed the single commandment of God. Their punishment which was told Adam before his transgression was thus meted out; Original Sin... spiritual and physical death, the spiritual taking place immediately at the moment Adam sinned and physical death began. And, due to his transgression/sin, Adam accrued guilt before God. The consequence of Adam's sin was passed on to ALL his progeny, i.e., every man, woman and child conceived on this earth inherits a depraved/corrupt nature (spiritually dead soul) and the guilt is imputed to them.
Okay, what does all this mean in regard to all who came into existence after the Fall? 1) Man's will is still free but it is subject totally to the fallen/corrupt/depraved nature. Since ALL MEN are spiritually dead, they by nature hate God, hate all things good and are at enmity with God. To summarize Paul's teaching in Romans 3, no man seeks after God. No man has one good thought. No man has a pure emotion. No man does anything good. Fallen man LOVES sin and everything evil. The non-Reformed religions ALL believe that man is NOT dead but terminally ill at worst. But there still resides within man the desire and ability to do that which is good although some believe that is only possible with God's help.
Now let us go back full circle. God has ordained/determined/decreed ALL THINGS, including the thoughts and intentions of every man woman and child. For example, God has ordained the assassination of leaders, the rape of women, the abortion of the unborn, the telling of lies, etc., etc., ad infinitum. But all these things which we are sinful and done by people according to God's ordination are done FREELY and most willingly because they are the NATURAL fruit of their depraved/corrupt nature. The biblical illustration I provided you with in regard to the crucifixion of Christ is the paradigm example, for there is no sin which anyone has done or could do is more horrid and worthy of eternal punishment that the murder of the incarnate Son of God, the man Christ Jesus. The crucifixion was ORDAINED and thus foretold in myriad prophesies through ancient times and by God's providence every single thing was orchestrated to bring this event about. Yet, ALL who participated in every tiny element throughout history did what they did most willingly... they chose to do so.
Conversely, if God does not decree all things and by His providence bring all things to pass, the world would immediately fall into complete ruin and the human race would annihilate itself in a very short time. Without the restraining power of God upon depraved humanity, ALL would be UTTERLY Depraved vs. Totally Depraved.
So, to iterate for you, since the Fall men are perfectly free to think, say and do as they
please according to their depraved/corrupt nature. They are NOT free to think, say or do anything contrary to that nature. (Rom 8:7,8; Eph 4:17,18; et al)
As God decreed thatJesus would die on the Cross, and yet God still used sinners to accomplish that thru their decisions, not forced by Him?
Explained above. God does not nor can He force the human will to do anything contrary to a person's nature. It took God's retraining providence to keep Christ alive until the perfect time (Gal 4:4,5). An illuminating incident in the OT shows a marvelous example of this truth (Gen 20:1-6).
The bible to me seems to be stating that in this Present age, before the second coming, There will be things permitted/allowed by God, sucj as Isis running wild for example?
My last time to state this for you.... ALL THINGS have been eternally decreed/foreordained/determined by God. ALL THINGS are under His infinite and perfect providential control and care. NOTHING happens nor can happen which God has not decreed. This truth is the foundation upon which a Christian rests his hope of eternal life and that he will forever be loved by God in Christ (Rom 8:28-39).