hello mamabeck!
First start by figuring out the names of the medications that your doctor is recommending you take for long term. Based on your description I am guessing he is leaning towards immunosuppressants before the biologics.
It's important that you keep an open dialog with your doctors. Ask what the severity of your disease is (what things look like on the inside), the risk of future complications, his/her suggestions for short term and long term treatment (ALL of your options) and what signs and symptoms you need to be on the lookout for currently to avoid any further complications.
Immunosuppressors do weaken your system. But the effects vary depending on the medication you are on and the dosage and the fact that everyone reacts to these medications in your own way. While it is possible you may get sick more frequently, it is also possible that you may not.
So to start, simply let your doctor know that you are uncertain about what is going on and what your options are and ask them to explain things a bit more clearly and detailed for you. You should then be able to take information from what they say that you can go home and research yourself to ask additional questions of your doctor and gather enough info to make the right decision based on your specific condition and your specific symptoms. Information about treating this disease can be a bit overwhelming and at the end of the day the decision on how to treat your crohn's is your decision. So make sure you understand what your options are starting with what your doctors are telling you.
Wishing you the best and hope you start to feel even better very soon!