So, if you don't use hybrid app designer to create Hybrid app , right ? ,If this is the case, you could invoke your mbo's object query ( such as findByParameter ) by looking at the doc section about use javascript APIs to access MBO at
basically, you need to generate js api by right click on your mobile application project and it should have menu "Generate Hybrid API..." , and it will start a wizard to generate apis which you could use them in your js code to invoke mbo's options.
Please let me know if you still have problem , or you could send me your sample code which could demo your problem to yan.gong@sap.com,