I am DMing a campaign set during the Thirty Years War. We are playing in the Pathfinder system, and I have made some custom rules for gunpowder.

With this post, I would like to invite your comments on how to proceed with the campaign and how to hook my quests up in a way that makes some kind of sense.

I next need my players to save a holy relic from a cathedral on the route of an advancing enemy army led by a general who intends to melt the precious metal from the relic's shrine into coins bearing anti-catholic slogans and distribute them among his soldiers as loot.

I'm not sure how the quest will look, but I was planning to have a face-off between the players and an advance party of the army, led by the tallest man in his time, der Lange Anton, who is a mercenary sergeant in the protestant army.

The question that I'm pondering is whether the protestant troops will already have conquered the city, which I assume must have at least a rampart defense, or whether the players (and the enemy advance party) will be sneaking into a city under siege.

[hider=Background]We start out in 1631 after the sack of Magdeburg and the battle at Breitenfeld.

The Swedish king Gustav Adolph has established himself as the de facto leader of the Protestant Union. The houses of Sachsen, Brandenburg and Baden-Baden have rallied to his side.

On the catholic side, the 70+ y.o.general of the Catholic League and the champion of king Maximillian I of Bavaria, Tilly, is a falling star. His destruction of Magdeburg, the strongest fortress in the north with the resulting massacre and his defeat at Breitenfeld are unacceptable.

The former general field marshal of the Holy Roman Empire, Wallenstein, will be reinstated to his former position after the winter of 1631.

It is currently September 1631. The players are Germans of various backgrounds and have signed up as mercenaries with the catholic mercenary general Heinrich Holck.

Holck is loyal to Wallenstein and speculated in Tillys defeat, not partaking in the battle of Breitenfeld. Holck is currently marching over the Erzgebirge into Bohemia, where he will meet with other generals in Karlsbad and take up winter quarters in Rakonitz near Prague.[/hider]

[hider=Events so far]
The players were fighting some marauders behind the marching army. After the battle, they found out that these were not simple marauding bandits, but professional soldiers of the army of Saxony, which advances on the Bohemian border city of Egen under the banner of the fanatic protestant general Christian the Mad ("der Tolle" Christian von Braunschweig-Wolfenbüttel).

The players made their way over an abandoned pass in the Erzgebirge. Here, they were assaulted by a werewolf, that had sought refuge in the forest pass. They are currently waiting for our next session. One or more players who failed the Fort saves may have contracted lycantropy.[/hider]

In our next session, the players will arrive at Karlsbad and bring the news to general Holck.
Because they looted silver coins from general Christians sack of Paderborn and the destruction of the holy relics kept there, clergymen in the staff will connect the dots and identify the advancing general.

The next side-quest will be to save the holy relics held at the Marienkirche in Plan, south of Eger. Plan is a mint city, and so it is likely that Christian will mark his succesful campaign into Bohemia by destroying the relics held there and generating commemorative propaganda tokens.

Two new players will be attached to the party. An exiled paladin inquisitor from the catholic city of Ellwangen, which is currently held by the Swedish army and the treacherous count of Hohenlohe-Neuenstein. The second addition to the party is a rogue who hails from Plan and will know a way to get into the city undetected. He may be joining in Karlsbad, or they may come across him on their way to Plan.

That's the plan so far. I hope you will give me some ideas on how to bring it all together in a way that makes narrative sense and offers the players a chance to play the game.

Later, the protestants will take Plan and the imperial army will march south to Wolfersdorf, in order to stop the enemy army from reaching Pilsen, the home of general Wallenstein.
In the valley of the river Thein, a major battle will ensue with sieges, trench warfare, artillery bombardments, scouting missions and an actual battle employing linear tactics of the era.

The players' mission will be to drive the army of Saxony out of Bohemia and to settle any personal scores that may have resulted from their side quests. This will also introduce commanders from both sides which will play significant roles in events to come.