Many thanks for the comments.
Are you saying that if I do the final positioning with OBMM, WB will not benefit from the BOSS Bash tags or will it be OK to run BOSS, OBMM for final Load Order and then run the WB bash feature?
Well you can do the load order with either OBMM, Wrye Bash (manually using Ctrl + Up/Down), or with BOSS. I just find it convenient to use OBMM first, run BOSS from Wrye Bash (hit the BOSS button at the bottom of Wrye Bash interface), then in your case I would then shuffle around your created mods which are not recognised by BOSS by highlighting them and using Ctrl + Up/Down.... then do the rebuild of Bashed patch.
If you re-arrange the load order after creating the bashed patch, things will be messed up because the bashed patch is a merge of tagged mods, and takes into account the order they were in before you build it. So however you choose to re-arrange your load order, it needs to be done before building the bashed patch.
@VargrReference archive invalidation in OBMM; The option I use is in Utilities / Archive invalidation / select BSA alteration
Also sorry missed your mention reference the saves....
In Wrye bash, after you have finished everything else (load order/rebuild), go to the saves tab, then left click on your save to be updated. On the right is a list of masters needed for that save, if you right click in that list you will get a prompt pops up, click on Okay, now you will notice under the masters list the save button is no longer ghosted, click it and your save is updated to the current masters list and should cause less problems playing from that point onwards (although its not guaranteed to work, sometimes changes to mods requires a complete game restart, but more often than not this little procedure helps these days)