Cisco VLAN

I'm confused on your setup.  This does not make sense:

--> "Switch A&B are connected via 2 uplinks Which are LACP LAG 1 is on the default Vlan the second Uplink LAG is set to access on both ends in Vlan 1000.  "

It sounds like you have two uplinks in a link access group, but each link is configured differently, which will not work.  Links in a LAG, must be the same.

So How are Switch A & B connected?  If you have multiple VLAN's on A and B that need to talk to each other, then the link between those switches must be a TRUNK in order to allow multiple VLAN's.

The only traffic on VLAN 1000 will be traffic that belongs on VLAN 1000.

Can you post the configuration for the links that connect switch A&B?

A simple question, just to make sure, is server 3 on the same IP subnet as server 1&2?

Sorry for the late replay was out yesterday and had an exchange issue today.   This I have two switches which are Cisco Sg200 series one in the front of the building on in the back on switch A there is a Hyper-V failover cluster consisting of two DL580 Nodes and a Storage server which houses all of the VHD’s the storage server is connected via Copper ISCSI.  On switch B is another DL580 which is the replica and has the autoloader connected to it.  Switch A and B have two uplinks consisting of multiple connections which have been put in a LAG via LCAP 1 and 2.  One is the production network 2 I want to use as the backup network and for replication.  On Switch A I have the following VLan’s
100–Production Network
200-Live Migration
300-Cluster Communication
400-ISCSI-1
500-ISCSI-2
600-ISCSI-3
1000-Backup Network

Switch B

100-Production Network
700-ISCSI-1
800-ISCSI-2
900-ISCSI-3
1000-Backup Network

Switch A LAGS

1-Production Uplink to Switch B
2-Backup Network Uplink to Switch B
3-Failover Cluster Node 1 LAG
4-Failover Cluster Node 2 LAG

Switch B LAGS

1-Production Uplink to Switch A
2-Backup Network Uplink to Switch A
3-DL580 Replica

All Vlan’s are set to except 100 are set to VLAN Mode Access.  100 is set to trunk.

I think you may be confused about a few things.  VLAN's are not set to access or trunk.  

Ports/LAG groups are set to access or trunk.

If you have a port/LAG set to access, then only 1 VLAN can have traffic flow in/out of that port/LAG and the frames are untagged.

If you have a port/LAG set to trunk, then multiple VLAN's can flow over that port/LAG and all frames are tagged with the VLAN id, execpt for the native VLAN.

Yes What I did is map the ports that the physical cables are plugged into say for Vlan 200 Cluster communication are on physical ports 2 and 20 I set them to Vlan 200 and then set the ports to Access.  Should I have not done that should I just leave everything as trunk and set the the the specific VLAN's in the setup I have there should be no need for any connections to be in more than one VLAN.

Both switches have VLAN 100 and VLAN 1000.   Therefor the uplinks between switch A and switch B must be defined as a trunk and they must allow VLAN 100 and VLAN 1000 over the trunk.  They don't need to allow any other VLAN's

I'm confused why you have two unique LAG's connecting the two switches.  You should only need one LAG with multiple ports.  The whole idea between a LAG is you have multiple physical port that logically act like one.  There is no reason to have two unique LAG's connecting the same pair of switches.  All the ports in one LAG will sit idle waiting for all the ports in the other LAG to fail.  So you have ports sitting there doing nothing.

There is no real reason for the the two uplink lags I just thought it may help cut the congestion to the clients some if all the backup and replication traffic was using a different link as the production network.  But since it is on the same switch and the switch is processing the traffic anyway it would not make a difference.

How many ports are in each uplink LAG?

LAG one has 3 copper and one fiber Lag two has 1 fiber and 1 copper

Yep You are Right Thanks for all of the help