Re: 2 Table Charity Tourney
The suggested format you are trying to use for this event does not fit well with your logistical circumstances.
I assume that you plan to have the final table played at a later time in the future, with tournament officials in charge of bringing the secured and appropriately-identified chip stacks for the eight prelimary table qualifying players to the final table.
Will the two qualifying events (at different venues) be occuring at the same time?
If yes, then both venues should be on the exact same time/blind schedule -- starting at the same time, with blind increases occurring simultaneously at both venue tables. If venue A gets down to four players first, then play at that table is suspended, and play continues at venue B until that table is down to four players. Blinds at the final table would start where they left off at venue B. Any chip discrepancies at the final table between the 8-player and 9-player table stacks would be minimal.
Pehaps a better way to advance eight players to the final table would not be the top four from each table, but the top eight remaining players once all other competing players have been eliminated (be it three remaining from venue A and five from venue B, or however it works out). The final table blinds would continue onward from the point where play was stopped (with eight total players remaining).
However, with this approach another problem can arise if you didn't get down to eight total players until one table had two players remaining and the other had six players remaining -- stack sizes would be very disappropriate at the final table. Even worse would be a "one player and seven players" scenario -- the lone player would have fully one-half of the chips in play at the final table.
This is why multiple-table tournaments are kept balanced by moving players to short tables, to keep the number of players (and chips, to some degree) equal at all tables, and to keep the number of hands played per hour somewhat constant at all tables. However, it doesn't sound like this is feasible in your proposed event, especially if the events are to be played on different days (or at different times).
My suggestion to you would be to run the event not as a freeze-out, but as a shoot-out. Play both tables down to a single player, then have those two players meet at the heads-up final table (with equal chipstacks). Start the final table blinds at whatever level seems appropriate for the stack sizes you choose (and you could start with any equal-size stacks -- same as the original tables, or the size stacks they had after winning their table).
This last approach eliminates all of your other logistical problems and issues completely.
Another advantage of the shootout format is that you can hold more than two qualifying table/events (if you choose), sending the winner of each to the final table. For example, you could hold two separate tournaments at each venue, and send four winners to the final table. You could also reduce the qualifying table size down to four (or six) players, sending the winner of each table to the finals.
Best of luck!