I don't have experience with Quartus, so treat this as general advice.
When working on paths between clock domains, timing tools expand the clocks to the least common multiple of their periods and select the closest pair of edges.
For paths from a 36 MHz clock (27.777 ns) to a 100 MHz clock (10 ns), if I did my quick calculations correctly, the closest pair of rising edges is 138.888 ns on the source clock and 140 ns on the destination clock. That's effectively a 900 MHz constraint for those paths! Depending on rounding (or for clocks with no relationship), it could come out worse than that.
There are at least three ways to write constraints for this structure. I am going to call the clocks fast_clk and slow_clk as I think that's clearer for illustration.
Option 1: disable timing with set_false_path
The easiest solution is to use set_false_path to disable timing between the clocks:
set_false_path -from [get_clocks fast_clk] -to [get_clocks slow_clk]
set_false_path -from [get_clocks slow_clk] -to [get_clocks fast_clk]
This is not strictly correct, since there are timing requirements for the synchronizer to work correctly. If the physical implementation delays the data too much relative to the control signal, then the synchronizer will not work. However, since there isn't any logic on the path, it's unlikely that the timing constraint will be violated. set_false_path is commonly used for this kind of structure, even in ASICs, where the effort vs. risk tradeoff for low-probability failures is more cautious than for FPGAs.
Option 2: relax the constraint with set_multicycle_path
You can allow additional time for certain paths with set_multicycle_path. It is more common to use multicycle paths with closely related clocks (e.g. interacting 1X and 2X clocks), but it will work here if the tool supports it sufficiently.
set_multicycle_path 2 -from [get_clocks slow_clk] -to [get_clocks fast_clk] -end -setup
set_multicycle_path 1 -from [get_clocks slow_clk] -to [get_clocks fast_clk] -end -hold
The default edge relationship for setup is single cycle, i.e. set_multicycle_path 1. These commands allow one more cycle of the endpoint clock (-end) for setup paths. The -hold adjustment with a number one less than the setup constraint is almost always needed when setting multi cycle paths, for more see below.
To constrain paths in the other direction similarly (relaxing the constraint by one period of the faster clock), change -end to -start:
set_multicycle_path 2 -from [get_clocks fast_clk] -to [get_clocks slow_clk] -start -setup
set_multicycle_path 1 -from [get_clocks fast_clk] -to [get_clocks slow_clk] -start -hold
Option 3: specify requirement directly with set_max_delay
This is similar to the effect of set_multicycle_path but saves having to think through the edge relationships and the effect on hold constraints.
set_max_delay 10 -from [get_clocks fast_clk] -to [get_clocks slow_clk]
set_max_delay 10 -from [get_clocks slow_clk] -to [get_clocks fast_clk]
You may want to pair this with set_min_delay for hold checks, or leave the default hold check in place. You may also be able to do set_false_path -hold to disable hold checks, if your tool supports it.
Gory details of edge selection for multi-cycle paths
To understand the hold adjustment that gets paired with each setup adjustment, consider this simple example with a 3:2 relationship. Each digit represents a rising clock edge:
1 2 3
4 5 6 7
The default setup check uses edges 2 and 6. The default hold check uses edges 1 and 4.
Applying a multi-cycle constraint of 2 with -end adjusts the default setup and hold checks to use the next edge after what they were originally using, meaning the setup check now uses edges 2 and 7 and the hold check uses edges 1 and 5. For two clocks at the same frequency, this adjustment makes sense — each data launch corresponds with one data capture, and if the capture edge is moved out by one, the hold check should also move out by one. This kind of constraint might make sense for two branches of a single clock if one of the branches has a large delay. However, for the situation here, a hold check using edges 1 and 5 isn't desirable, since the only way to fix it is to add an entire clock cycle of delay on the path.
The multi-cycle hold constraint of 1 (for hold, the default is 0) adjusts the edge of the destination clock uesd for hold checks backwards by one edge. The combination of 2-cycle setup MCP and 1-cycle hold MCP constraints will result in a setup check using edges 2 and 7, and a hold check using edges 1 and 4.
Best Answer
Since you use a PLL to generate your 12.5MHz clock, the phase relationship will be kept by the synthesis tool, whatever it is. This means the timing analysis will properly report any path between the two clocks and will tell you if it can't satisfy the setup/hold relationship. The clocks will also likely be edge-aligned, but this depends on the PLL's configuration.
It is easy to perform a clock-domain transfer between an edge-aligned 12.5MHz to 125MHz. If the source setup within 8ns, the 125MHz will latch the value without problem. The other direction is also easy, except you must keep any value for 10 125MHz clock-cycles to make sure the slower clock latch the new value (the tool won't verify this).
It is sometimes preferable to consider the two clocks asynchronous. An example case would be if the clock ratio is 11/13, it may be impossible to satisfy timings between the clocks. In that case, just consider them asynchronous, put false path constraints and use FIFOs, synchronization registers or any other technique to transfer data.
In your case, consider them synchronous, it shouldn't be difficult to meet timings if they are edge-aligned or if their phase relationship isn't utterly bad. Also be sure to verify the timings report, if the cross-domain paths aren't there, then you know there is something wrong.