If you cannot come up with a single table layout which can accommodated all of the players interested in your Apocalypse game you essential have two options. One is Split Table were you essentially have 2 games of apocalypse on 2 different large tables sharing an overall objective count and perhaps some way to transfer between the tables(webway, warp rift, bridge, etc.). This idea is relatively simple with the main question of how many total objectives and how to distribute them between the tables. The other is Side Tables. A side table is going to be smaller than the main table. It may have an objective for the main total or it may influence the main table through some other mechanism.
An example of a side table can be found in Apocalypse Reloaded where space marines assault an Ork Space Kill Kruzer which is dropping bombardments on the main table.
In our recent 40K point game we had two side tables. The side tables were 4*6 with 1 player from each team with 3000 points. Like our main table these were pretty densely occupied with 6000 points on a 4*6. The side tables influenced the main game by allowing whoever controlled a centrally located objective using 5th ed scoring rules at the end of a game turn to give a orbital bombardment to their main table teammates to place. The deployment was done using standard Apocalypse rules with the scatter die determining how the table was divided and 12 inch no mans land separating the deployment zones.
No one at the side tables used any Apocalypse formations by chance at one table and by gentleman's agreement for the other. One table used their assets while the other transfered them to the main table. There were also no superheavies, flyers, or gargantuan creatures on the side tables. Given that their was only a single objective at the center of the table any super heavy could have just rolled up on top of it and been very hard to remove. Also people wanted the superheavies on the main table where the game was going to won or lost since their were only 3 superheavies in the 40K of points. While this makes the games less Apocalypse like, it makes them a little more balanced.
The problem that was encountered on the Side-Main interaction scheme was the major advantage it gave to the player going second in the turns. In a normal game, the second player can try to grab objectives or contest at the very end of the game, but the player going first has 5 turns to remove those fast units and establish clear zones, etc. In the normal game it is an advantage that shows up only at the final ending moment. In this setup, the advantage appears every single turn. Even if you table your opponent on turn 5, if he controlled the objective for more than 1 turn earlier in the game he has essentially won the table for his main table comrades. With 3000 points fighting over 1 centrally located objective, pretty much anything the player going first places on the objective will be targeted and eliminated by the opponent or at least contested. This is especially true since the objective is only 6 inches off the deployment line. If the first player wants to hold the objective for the turn, he will have to probably completely cover it with models and build a wall of units around it into the opponents deployment zone.
This pretty much forces the player going first to essential go all in every turn. Certain armies will do better with this than others. One of the tables was Codex SM going first with Tyranids going second. It does not take much to surmise that the tyrnaids with there many assault and close range specialists had a distinct advantage in this setup. If the space marines want to hold that objective 6 inches from the Nid deployment line they will need some serious hitting force. This was compounded by the bid system carried over from the main table. The main table bids were 2 minutes and 30 minutes so the player going first on the side tables which is a disadvantage in this case only had 2 minutes to place his units.
The other side table was Codex Space Marines(me) vs Necrons. The Necrons were going second but were hindered by having very poor in assault warriors as their objective holders. I made the mistake of deploying my scoring units to far on the flanks. I forgot to play the specific mission in my rushed deployment again 2 minutes. The necron warriors did not stand up to my Pedro led rhino mounted Vanguard assault unit who managed in one turn sweeping advance away 2 units of warriors with a Orb Lord through a multiple assault. This was certainly a case of all in where my Pedro + 8 Vanguard charged 2 units each with about 15 warriors each plus the Lord. We both very quickly lost all our scoring units so the fighting was abandoned by agreement after the 3rd turn. The Necrons were able to generate 1 bombardment after destroying 2 vehicles contesting the objective at the end of the second turn.
Future Plan: Side Tables Rules
I think a better plan is needed for side tables in the future. Since we had 2 side tables, it might have made sense to look at asymmetric objective type missions similar to the old nonstandard Battle Missions. Each side could have a table with an attacker and a table with a defender. You could use could use either 1 objective placed by defender or something like 3 bunkers which each give a 2 blasts on the orbital bombardment for the main table when held by defender. These would probably work best with no Apoc datasheets or formations. It should be looked at as a good chance to get some nonstandard mission played. Here you would not use the main table turn order but let the attacker go first like in these battles normally.
If you are only running 1 side table, you can play one of these nonstandard asymmetric missions with the attacking side getting a few extra assets of. You could also do a dawn of war or pitched battle for deployment with the two objective standard mission. Each objective controlled gives the Apoc bombardment (3). This would also be without Apoc datasheets. The player going second still has a distinct advantage but the player going first has a better chance of holding their home objective than controlling a centrally located one. Also if the deployment time is not limited by the main table bids the playing going first is helped some.