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If your mod is creating surface that should not have any ore spawned then there are two ways to make RSO ignore it.
First one is to call following method: Which will stop RSO from spawning ores on given surface.
Second method is to use map settings that have resource sizes set to 0 - this disables spawning of given resource and can be used to selectively remove resources from surface.

It is recommended to start a new game, but regenerating resources in an old save is totally possible.
Map generation settings are read by the mod and used (from version for 0.12).

If you want to use old save or just want to regenerate the resources on map:

Use the following command to regenerate resources: Regenerate resources only on current surface, you can add all as parameter to regen also starting area (can be useful to get tungsten patch on Vulcanus that was added in 7.0.3).
Regenerates resources on all surfaces (ignores starting areas).
You can add noenemies to the command to only regenerate resources and leave enemy bases as is.

To change a seed to preffered value (use any number up to around 2000000000, due to factorio rng small values < 200 might net similar or identical results): There is also a command to only clear current resources/enemies: It also accepts noenemies as parameter to clear only resources.

If you want to change region size then recommended procedure is:
1. Call the clear command
2. Change the region size to new value in settings
3. Call the regenerate command

Be aware that this can take few minutes and biter bases might also respawn (depends on noenemies parameter). Safest place to execute this command is the starting area.
Any resources in the starting region are not affected by this command.

From version 5.0.8 RSO supports starting location reading from map settings. It will automatically create starting location on positions from map settings when surface is created.
To prevent that following call can be made before creating a surface: This will stop RSO from creating new starting areas.

Multiple starting areas handling is available from version 2.2.0.
Recommended way to use it is following:
1. Prepare all players/forces (RSO doesn't handle player setup, but you can use a mod like SpaceBook to manage this)
2. Chart big map area and select your starting locations using following command (size can be change as desired): 3. Call newly added clear command to clean up all biters/resources 4. Use new command to add start locations in desired places. Command looks as follows: Where x and y are coordinates in tiles of new start location (visible in top left usually in F5 debug menu).
Player that runs this command from console will get feedback about location creation (can fail if it's to close to different start location).
You can also specify the player as next parameter after position - output will be sent to that player then.
One drawback thats very difficult to fix currently is that new starting area location should be charted already. With default config and normal starting area size area is 448x448 centered on given position. If this area is not charted resources will be spawned but placement checks will not work correctly so they might end up on water.
5. Use standard regenerate command to generate resources/biters on rest of the map.
You can skip the clear and regenerate steps without problems with one drawback - each new starting area changes generator a bit so regeneration called after adding new start area might yield completely different results then initial generation. All starting areas are safe during clear and regenerate command and resources in them won't be changed.

Basic resource configuration is affected by three main settings: absolute_resource_chance,global_richness_mult and starting_richness_mult.
They can be used to change resource frequency (per region) and amount of resources in each node respectively. Starting richness multiplier affects only starting area, global one affects all the resources outside starting area.
Resource richness increase from distance to center is controlled separately by richness_distance_factor.

Additionally there is a feature that can generate another resource next to main resource in region - it is controlled by resource specific configuration and three multi_resource_ factors described in config file.

If any of endless resource mods or options of other mods is activated then RSO will try to detect changed resources and apply special size modifier for them as defined by endless_resource_mode_sizeModifier setting.

Main option controlling biters distribution are absolute_enemy_chance and enemy_base_size_multiplier. They are similar to resource ones and state chance of biter bases per region and multiplier to their size.
You can enable/disable enemy expansion from config using disableEnemyExpansion option. Expansion is enabled by default which means biters will migrate towards the empty areas. You can disable it for more paceful game and easier exploration.
There is also an option to change distribution of biter vs spitter ration by using biter_ratio_segment and spitter_ratio_segment.

RSO will try to integrate with bob's enemies and will also use spawners added by it. Additional enemies added by DyTech are not affected by base spawning.
For integration with peacemod RSO will automatically drop enemy spawns when it's detected. If you still want enemies this behavior can be overridden with useEnemiesInPeaceMod setting.