This requires Arcane Dimensions. - mukor

Picking up a bomb targets the first set of trigger_counters, "bomb_count".

each "bomb_count" has a different count required to then trigger a trigger_relay, "sites_on_1", "sites_on_2", "sites_on_3".

Each "sites_on_X" targets a trigger_entity_state_on(sites_on_trigger) placed by each bombsite that then targets the respective bombsite trigger_once, "site_a", "site_b", site_c", turning the trigger_once volumes on.

"site_on_x" ALSO(through the use of Arcane Dimensions 'target2' key) target a trigger_counter, "bomb_count_1", "bomb_count_2", "bomb_count_3". 

"sites_on_X" ALLLLSO killtarget the "bomb_count_X" below it. (sites_on_2 kills bomb_count_1, sites_one_3 kills bomb_count_2, and so on.) 

Each "bomb_count_X" has the spawnflag "Start OFF" enabled. Now that it has been targeted, is it turned on and will start counting once it is targeted again.

Once each "bomb_count_X" is triggered enough, it will turn off all the bomb sites, waiting for the player to pick up another bomb, or because all the bombs have been picked up.

When the player walks into the trigger_once for "site_a/b/c", it targets a series of tigger_relays all named after their respective bombsite, "site_a_relay","site_b_relay","site_c_relay". Each "site_a/b/c_relay" targets bomb_count_1/2/3, its respective misc_model bomb model (bomb_a/b/c), its respective ambient_custom_sound, "bomb_planted_a/b/c", and finally a trigger_relay with a delay that targets a trigger_explode, "bomb_a/b/c_explode" respective to each site.

Each bombsite then killtargets itself so as not to be turned back on when the "sites_on_X" relay is targeted again.

What all this means is you can pick up one bomb at a time and plant it on any given bombsite. You could pick up two and then plant one, pick up the remaining bomb then plant the final two. You could pick up all three and place them all. 

To add more bombs you can copy all the entities that make up the bomb sites, past them into a text editor and replace all instances of "_X" (where X is the bomb site letter) with a new letter. Then copy the top row of trigger_counters/relay, paste into a text editor and increment everything by one.