If you ask a dozen players you will get a dozen and a half answers for sure
I like to blockade the South as much as I can. As grimjaw stated, those Blockade Flotillas missing Blockade ships should have the Blockade ships replace. It takes about 2 turns per Blockade ship with the Flotilla in a large harbor in Passive Posture--left side of RoE (Rules of Engagement) green--to pickup and complete building a replacement ship. During this time the Flotilla is locked in harbor.
Once the Flotillas are up to full strength I send them into the Blockade Boxes. Keep the Flotillas in the Blockade Boxes divided up between the two boxes as evenly as possible.
Insure that you have at least 2 transport per box to keep the Flotillas supplied. Nearly always on transport squadron will be used to supply the Blockade Flotillas in one Blockade Box at a time. Once either its GS or Ammo has reached nearly 0, send it back to harbor to resupply. From the Atlantic Blockade Box I sent them back to New York City, from the Gulf Blockade Box I send them generally to Fort Pickens, but that will depend on the situation there. Alternatively you can sent them to Forts Jefferson and Zachary. If you find the supplies in the forts are not keeping up with what is needed build a couple of transports squadrons to use to build a depot in one of the forts.
In AACW I used to always put all the Blockade Squadrons and transports in 1 stack. In CW2 I have the feeling that when a single stack of Blockade Flotillas fights a blockade runner, ALL of the ships in the stack take a lot of cohesion loss even though most of them could not even be involved in the combat. To alleviate this I've stated giving each Blockade Flotilla its own transport squadron and put each of these pairs into its own stack. The Blockade Flotillas can carry enough supplies to get along without their transports for a couple of turns, so barring any major hiccups in resupplying the transports I haven't seen any issues with this of yet.
I would not suggest using the Blockade Flotillas to patrol the East Coast rivers. They are too expensive for that duty, plus you only need 4 naval combat elements to block land units--maximum of a 90% chance--from crossing a river.
If you want to patrol the rivers on the East Coast build gunboats of 2 squadron fleets--4 gunboat elements--, each with 1 riverine transport squadron, and use those liberally. It's also a good idea to build a couple of Monitor/Timberclad fleets to guard them. Since having your patrols in Offensive Posture will wear them down very quickly and they can still block crossings in Defensive Posture you will want do that. But that also means that CS fleets in DP can sail right past these patrols. That's where your guards come into play. Leave those on the exposed end of the river in DP. If a CS fleet in OP enters the river it will have to attack your guarding fleet. If it sails by in DP, you will have 1 turn to send your guard-fleet after them. Even if in the next turn they might manage to knock your patrol fleet out of its river region, you still have some days for your guard fleet to reach that region and attack the CS fleet before any land units can complete a crossing.
The Pacific Fleet in San Francisco only unlocks if attacked--far from likely--or if FI (Foreign Intervention) goes over 100 and Great Britain and France enter the war. In the latter case you will wish you had built lots of ships while you had the chance as the fleet of these factions will wreak havoc on your shipping and blockades and generally anything they find. Often they will post themselves in the Atlantic in front of New York City to intercept any traffic heading into or out of the North Atlantic OMB (Off-Map-Box).
So if FI goes up to 60-70 and you think it might continue to raise, you better start build more warships.
As far as the Far West goes, I'm not that confident of what to do there. If you want to invest LOTS of money, you can put a depots in each of the OMB's to have the abundant supplies on the West Coast move into Western New Mexico and supply a troop buildup there. You can even build a road all the way, but it will take many, many turns. You should probably improve the regions between North-Western NM and Kansas so that at least one line of stockades has at least "track" along the entire route to assist in supplies flowing from the Kansas-Missouri-Iowa area. There are 4 regions that need tracks along the southern edge of the IT.
If you want to know how to send troops from the West Coast toward the east, the best way is to just drag them from their current location to where you want them to end and check their paths. Generally those coming form Oregon I send to Denver and those further south I send through Southern California.
Put all those troops you are sending on such long marches into PP (Passive Posture) as long as they are far enough away from any enemies--generally all of the time until they actually reach the map and even on the map up around Colorado--, so that they will loose the least cohesion on their multi-turn marches; set them to Enter Structure at the end of their march so that they will start recovering cohesion as soon as the arrive in a region, even if it's in the middle of the turn. Also DO NOT stack them together! If you stack them, the entire stack will suffer from a huge lack of CP's and will be that much slower and lose cohesion that much faster. Plot moves that will put them inside a town or stockade before they have marched too far--about 2-3 turns in general, least they wear them selves down too far and take forever to make any progress.
Once Carson and Carlton are unlocked try to use those 2 in their own stack; build a division, even if it's a small one. They have high strategic ratings and will remain active most of the time, but they are about the lowest in seniority of all of your leaders. Stacking them with Canby or other leaders with higher rank/seniority will only cause them to be inactive much of the time.
If you want, you can use one of the Training Officers, such as Franz Sigel, to train up all those militia you get in the Far West, but of course then you can't use him in the east for that.
I can't really say much more with very much certainty on the Far West. It can be a money and troop vortex if you let it so you will have to use your best judgement.
And don't forget the sun screen
