For Cylon attack cards, what happens if you already have some of the ships that would be deployed to the table already on the table? For example, if you already have 2 base stars on the table and you draw a crisis card with more base stars, do the existing base stars on the table move to the new position on the crisis card or do they stay where they are? Or if you have only 1 base star on the table and you draw a crisis card that puts 2 on the table, where do you put your 2nd base star since there are 2 new positions for that unit?

My 2nd question has to do with combat. Let's say there are 5 raiders, 1 Vyper, and 1 civilian ship in a space area and Raiders get activated. Per the rules, the Raiders shoot at the Vyper. Do all 5 attacks from the Raiders happen simultaneously against the Vyper? Or do you roll them 1 at a time, allowing the Raiders to destroy the civilian ship if one of the earlier rolls damages or destroys the Vyper, thus leaving the Raiders with no other target but the civilian ship?

I think the first question can be decided by house rules. Generally when I play, if both base stars are out when a card setting up another base star is drawn, we ignore that part of it and set up what we can. This is the same for when we run out of raiders/heavy raiders.

For your second, you roll one at a time. If the first raider destroyed the viper, the second would automatically destroy the civvie ship, and the remaining three would travel towards the nearest civvie ship.