For the first question, the Commander ability specifies that the formations need to be within 5cm. When off-table, formations won't meet those criteria, and thus won't be able to use or benefit from the Commander ability.
For the second question part one, from the FAQ:
FAQ wrote:
Q: Can a formation enter play via a Webway Portal that is covered by, or is in the zone of control of, enemy units?
A: Yes, but the formation using it to enter play would have to carry out an engage action.
Q: What happens when a formation in reserve fails its action test and needs to enter play via a Webway Portal that is covered by, or is in the zone of control of, enemy units?
A: It takes a Blast marker, and may not take a hold action. It effectively looses its activation.
And if you can only place some of the units, my guess is that this rule should then apply:
1.7.4 Formations wrote:
Any units that are out of formation for any reason after a formation has taken the movement part of its action are destroyed. The controlling player may choose which units are out of formation and destroyed. Note that each unit lost will place one Blast marker on the main part of the formation. This applies after each individual move, so if a formation made a march action, you can’t wait until the end of all three moves in order to bring units back into formation—any out of formation units are destroyed at the end of the first move (and again at the end of the second and third moves if any other units have also ended up out of formation following the move).